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Wu Y, Feng J, Zhang Q, Wang Y, Guan Y, Wang R, Shi F, Zeng F, Wang Y, Chen M, Chang J, He G, Yang G, Li Y. Integrative gene duplication and genome-wide analysis as an approach to facilitate wheat reverse genetics: An example in the TaCIPK family. J Adv Res 2024; 61:19-33. [PMID: 37689241 DOI: 10.1016/j.jare.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023] Open
Abstract
INTRODUCTION Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. OBJECTIVE To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. METHODS We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial-temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. RESULTS As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPKs from seven monocot species, established the orthologous relationship of CIPKs between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g., CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBLs and TaCIPKs could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. CONCLUSION The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat.
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Affiliation(s)
- Ya'nan Wu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Jialu Feng
- Hubei Provincial Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qian Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yanbin Guan
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Ruibin Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fu Shi
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fang Zeng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
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Fu YB. Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ. Int J Mol Sci 2024; 25:5930. [PMID: 38892116 PMCID: PMC11172543 DOI: 10.3390/ijms25115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide is a challenging mission. The extent of deleterious mutations present in conserved germplasm and the genetic risk associated with accumulative mutations are largely unknown. This study took advantage of published barley genomic data to predict sample-wise mutation burdens for 19,778 domesticated barley (Hordeum vulgare L.) accessions conserved ex situ. It was found that the conserved germplasm harbored 407 deleterious mutations and 337 (or 82%) identified deleterious alleles were present in 20 (or 0.1%) or fewer barley accessions. Analysis of the predicted mutation burdens revealed significant differences in mutation burden for several groups of barley germplasm (landrace > cultivar (or higher burden estimate in landrace than in cultivar); winter barley > spring barley; six-rowed barley > two-rowed barley; and 1000-accession core collection > non-core germplasm). Significant differences in burden estimate were also found among seven major geographical regions. The sample-wise predicted mutation burdens were positively correlated with the estimates of sample average pairwise genetic difference. These findings are significant for barley germplasm management and utilization and for a better understanding of the genetic risk in conserved plant germplasm.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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Liu Y, Li H, Liu J, Wang Y, Jiang C, Zhou Z, Zhuo L, Li W, Fernie AR, Jackson D, Yan J, Luo Y. The additive function of YIGE2 and YIGE1 in regulating maize ear length. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38804053 DOI: 10.1111/tpj.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement.
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Affiliation(s)
- Yu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Huinan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jie Liu
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ziqi Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Ghorbel M, Zribi I, Haddaji N, Siddiqui AJ, Bouali N, Brini F. Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae. PLANTS (BASEL, SWITZERLAND) 2023; 13:11. [PMID: 38202319 PMCID: PMC10781083 DOI: 10.3390/plants13010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.
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Affiliation(s)
- Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Ikram Zribi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Arif Jamal Siddiqui
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Nouha Bouali
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
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Mu W, Li K, Yang Y, Breiman A, Yang J, Wu Y, Zhu M, Wang S, Catalan P, Nevo E, Liu J. Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum. Mol Biol Evol 2023; 40:msad259. [PMID: 38000891 PMCID: PMC10708906 DOI: 10.1093/molbev/msad259] [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: 07/06/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kexin Li
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Adina Breiman
- Department of Evolutionary and Environmental Biology, University of Tel-Aviv, Tel-Aviv 6997801, Israel
| | - Jiao Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ying Wu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pilar Catalan
- Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca 22071, Spain
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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Puccio G, Ingraffia R, Giambalvo D, Frenda AS, Harkess A, Sunseri F, Mercati F. Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families. FRONTIERS IN PLANT SCIENCE 2023; 14:1302337. [PMID: 38023895 PMCID: PMC10665861 DOI: 10.3389/fpls.2023.1302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.
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Affiliation(s)
- Guglielmo Puccio
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Dario Giambalvo
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alfonso S. Frenda
- Department of Agricultural, Food and Forestry Sciences, University of Palermo, Palermo, Italy
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Francesco Sunseri
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
- Department Agraria , University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Francesco Mercati
- Institute of Biosciences and BioResources (IBBR), National Research Council, Palermo, Italy
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Li T, Luo K, Wang C, Wu L, Pan J, Wang M, Liu J, Li Y, Yao J, Chen W, Zhu S, Zhang Y. GhCKX14 responding to drought stress by modulating antioxi-dative enzyme activity in Gossypium hirsutum compared to CKX family genes. BMC PLANT BIOLOGY 2023; 23:409. [PMID: 37658295 PMCID: PMC10474641 DOI: 10.1186/s12870-023-04419-0] [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: 02/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Cytokinin oxidase/dehydrogenase (CKX) plays a vital role in response to abiotic stress through modulating the antioxidant enzyme activities. Nevertheless, the biological function of the CKX gene family has yet to be reported in cotton. RESULT In this study, a total of 27 GhCKXs were identified by the genome-wide investigation and distributed across 18 chromosomes. Phylogenetic tree analysis revealed that CKX genes were clustered into four clades, and most gene expansions originated from segmental duplications. The CKXs gene structure and motif analysis displayed remarkably well conserved among the four groups. Moreover, the cis-acting elements related to the abiotic stress, hormones, and light response were identified within the promoter regions of GhCKXs. Transcriptome data and RT-qPCR showed that GhCKX genes demonstrated higher expression levels in various tissues and were involved in cotton's abiotic stress and phytohormone response. The protein-protein interaction network indicates that the CKX family probably participated in redox regulation, including oxidoreduction or ATP levels, to mediate plant growth and development. Functionally identified via virus-induced gene silencing (VIGS) found that the GhCKX14 gene improved drought resistance by modulating the antioxidant-related activitie. CONCLUSIONS In this study, the CKX gene family members were analyzed by bioinformatics, and validates the response of GhCKX gene to various phytohormone treatment and abiotic stresses. Our findings established the foundation of GhCKXs in responding to abiotic stress and GhCKX14 in regulating drought resistance in cotton.
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Affiliation(s)
- Tengyu Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kun Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Chenlei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lanxin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jingwen Pan
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Mingyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, 450001, China
| | - Jinwei Liu
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, 450001, China.
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Ma J, Wang R, Zhao H, Li L, Zeng F, Wang Y, Chen M, Chang J, He G, Yang G, Li Y. Genome-wide characterization of the VQ genes in Triticeae and their functionalization driven by polyploidization and gene duplication events in wheat. Int J Biol Macromol 2023:125264. [PMID: 37302635 DOI: 10.1016/j.ijbiomac.2023.125264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.
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Affiliation(s)
- Jingfei Ma
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Ruibin Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Hongyan Zhao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Li Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Fang Zeng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
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10
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Han L, Zhong W, Qian J, Jin M, Tian P, Zhu W, Zhang H, Sun Y, Feng JW, Liu X, Chen G, Farid B, Li R, Xiong Z, Tian Z, Li J, Luo Z, Du D, Chen S, Jin Q, Li J, Li Z, Liang Y, Jin X, Peng Y, Zheng C, Ye X, Yin Y, Chen H, Li W, Chen LL, Li Q, Yan J, Yang F, Li L. A multi-omics integrative network map of maize. Nat Genet 2023; 55:144-153. [PMID: 36581701 DOI: 10.1038/s41588-022-01262-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/03/2022] [Indexed: 12/31/2022]
Abstract
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Here, we constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. We applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks. We validated the functions of 20 genes, including 18 with previously unknown connections to flowering time in maize. Furthermore, we uncovered a flowering pathway involving histone modification. The multi-omics integrative network map illustrates the principles of how molecular networks connect different types of genes and potential pathways to map a genome-wide functional landscape in maize, which should be applicable in a wide range of species.
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Affiliation(s)
- Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jia Qian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Peng Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonghao Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Babar Farid
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture Multan, Multan, Pakistan
| | - Ruonan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zimo Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhihui Tian
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Sijia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qixiao Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaxin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaomeng Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chang Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xinnan Ye
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hong Chen
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Weifu Li
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
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11
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Kasemsap P, Bloom AJ. Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 12:85. [PMID: 36616214 PMCID: PMC9823454 DOI: 10.3390/plants12010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.
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12
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Sun P, Jiao B, Yang Y, Shan L, Li T, Li X, Xi Z, Wang X, Liu J. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. MOLECULAR PLANT 2022; 15:1841-1851. [PMID: 36307977 DOI: 10.1016/j.molp.2022.10.018] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/19/2022] [Accepted: 10/23/2022] [Indexed: 05/25/2023]
Abstract
Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth. To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses, there is a need for convenient and accurate toolkits. To meet this need, we developed WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi). As an example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.
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Affiliation(s)
- Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Beibei Jiao
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Lanxing Shan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ting Li
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Xiaonan Li
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiyin Wang
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China.
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China; State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
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13
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Mou Y, Yuan C, Sun Q, Yan C, Zhao X, Wang J, Wang Q, Shan S, Li C. MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:980933. [PMID: 36340369 PMCID: PMC9631947 DOI: 10.3389/fpls.2022.980933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.
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14
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Winichayakul S, Curran A, Moraga R, Cookson R, Xue H, Crowther T, Roldan M, Bryan G, Roberts N. An alternative angiosperm DGAT1 topology and potential motifs in the N-terminus. FRONTIERS IN PLANT SCIENCE 2022; 13:951389. [PMID: 36186081 PMCID: PMC9523541 DOI: 10.3389/fpls.2022.951389] [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: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The highly variable cytoplasmic N-terminus of the plant diacylglycerol acyltransferase 1 (DGAT1) has been shown to have roles in oligomerization as well as allostery; however, the biological significance of the variation within this region is not understood. Comparing the coding sequences over the variable N-termini revealed the Poaceae DGAT1s contain relatively high GC compositional gradients as well as numerous direct and inverted repeats in this region. Using a variety of reciprocal chimeric DGAT1s from angiosperms we show that related N-termini had similar effects (positive or negative) on the accumulation of the recombinant protein in Saccharomyces cerevisiae. When expressed in Camelina sativa seeds the recombinant proteins of specific chimeras elevated total lipid content of the seeds as well as increased seed size. In addition, we combine N- and C-terminal as well as internal tags with high pH membrane reformation, protease protection and differential permeabilization. This led us to conclude the C-terminus is in the ER lumen; this contradicts earlier reports of the cytoplasmic location of plant DGAT1 C-termini.
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Affiliation(s)
- Somrutai Winichayakul
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Amy Curran
- ZeaKal Inc., San Diego, CA, United States
| | - Roger Moraga
- Bioinformatics and Statistics, AgResearch Ltd., Palmerston North, New Zealand
| | - Ruth Cookson
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Tracey Crowther
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Marissa Roldan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Greg Bryan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
| | - Nick Roberts
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
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15
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Phylogenomics and Systematics of Overlooked Mesoamerican and South American Polyploid Broad-Leaved Festuca Grasses Differentiate F. sects. Glabricarpae and Ruprechtia and F. subgen. Asperifolia, Erosiflorae, Mallopetalon and Coironhuecu (subgen. nov.). PLANTS 2022; 11:plants11172303. [PMID: 36079685 PMCID: PMC9460391 DOI: 10.3390/plants11172303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Allopolyploidy is considered a driver of diversity in subtribe Loliinae. We investigate the evolution and systematics of the poorly studied Mesoamerican and South American polyploid broad-leaved Festuca L. species of uncertain origin and unclear taxonomy. A taxonomic study of seven diagnostic morphological traits was conducted on a representation of 22 species. Phylogenomic analyses were performed on a representation of these supraspecific taxa and all other Loliinae lineages using separate data from the entire plastome, nuclear rDNA 45S and 5S genes, and repetitive DNA elements. F. subgen. Mallopetalon falls within the fine-leaved (FL) Loliinae clade, whereas the remaining taxa are nested within the broad-leaved (BL) Loliinae clade forming two separate Mexico–Central–South American (MCSAI, MCSAII) lineages. MCSAI includes representatives of F. sect. Glabricarpae and F. subgen. Asperifolia plus F. superba, and MCSAII of F. subgen. Erosiflorae and F. sect. Ruprechtia plus F. argentina. MCSAII likely had a BL Leucopoa paternal ancestor, MCSAI and MCSAII a BL Meso-South American maternal ancestor, and Mallopetalon FL, American I–II ancestors. Plastome vs. nuclear topological discordances corroborated the hybrid allopolyploid origins of these taxa, some of which probably originated from Northern Hemisphere ancestors. The observed data indicate rapid reticulate radiations in the Central–South American subcontinent. Our systematic study supports the reclassification of some studied taxa in different supraspecific Festuca ranks.
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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17
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Yamamoto N, Tong W, Lv B, Peng Z, Yang Z. The Original Form of C 4-Photosynthetic Phospho enolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905894. [PMID: 35958195 PMCID: PMC9358456 DOI: 10.3389/fpls.2022.905894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Poaceae is the most prominent monocot family that contains the primary cereal crops wheat, rice, and maize. These cereal species exhibit physiological diversity, such as different photosynthetic systems and environmental stress tolerance. Phosphoenolpyruvate carboxylase (PEPC) in Poaceae is encoded by a small multigene family and plays a central role in C4-photosynthesis and dicarboxylic acid metabolism. Here, to better understand the molecular basis of the cereal species diversity, we analyzed the PEPC gene family in wheat together with other grass species. We could designate seven plant-type and one bacterial-type grass PEPC groups, ppc1a, ppc1b, ppc2a, ppc2b, ppc3, ppc4, ppcC4, and ppc-b, respectively, among which ppc1b is an uncharacterized type of PEPC. Evolutionary inference revealed that these PEPCs were derived from five types of ancient PEPCs (ppc1, ppc2, ppc3, ppc4, and ppc-b) in three chromosomal blocks of the ancestral Poaceae genome. C4-photosynthetic PEPC (ppcC4 ) had evolved from ppc1b, which seemed to be arisen by a chromosomal duplication event. We observed that ppc1b was lost in many Oryza species but preserved in Pooideae after natural selection. In silico analysis of cereal RNA-Seq data highlighted the preferential expression of ppc1b in upper ground organs, selective up-regulation of ppc1b under osmotic stress conditions, and nitrogen response of ppc1b. Characterization of wheat ppc1b showed high levels of gene expression in young leaves, transcriptional responses under nitrogen and abiotic stress, and the presence of a Dof1 binding site, similar to ppcC4 in maize. Our results indicate the evolving status of Poaceae PEPCs and suggest the functional association of ppc1-derivatives with adaptation to environmental changes.
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Affiliation(s)
- Naoki Yamamoto
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Wurina Tong
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Bingbing Lv
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang College, Xichang, China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
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18
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Yu S, Dong H, Fang T, Wu Y. Comparative analysis reveals chromosome number reductions in the evolution of African bermudagrass ( Cynodon transvaalensis Burtt-Davy). Genome 2022; 65:341-348. [PMID: 35850549 DOI: 10.1139/gen-2021-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
African bermudagrass (Cynodon transvaalensis Burtt-Davy) (2n = 2x = 18) belongs to the genus Cynodon, tribe Cynodonteae, subfamily Chloridoideae in the grass family Poaceae. The species is frequently crossed with common bermudagrass (Cynodon dactylon Pers.) in developing high-quality hybrid turf cultivars. Molecular resources for C. transvaalensis are scarce; thus, its genomic evolution is unknown. Recently, a linkage map consisting of 1278 markers provided a powerful tool for African bermudagrass genomic research. The objective of this study was to investigate chromosome number reduction events that resulted in the nine haploid chromosomes in this species. Tag sequences of mapped single nucleotide polymorphism markers in C. transvaalensis were compared against genome sequences of Oropetium thomaeum (L.f.) Trin. (2n = 2x = 20), a genomic model in the Cynodonteae tribe. The comparative genomic analyses revealed broad collinearity between the genomes of these two species. The analyses further revealed that two major interchromosomal rearrangements of the paleochromosome ρ12 (ρ1-ρ12-ρ1 and ρ6-ρ12-ρ6) resulted in nine chromosomes in the genome of C. transvaalensis. The findings provide novel information regarding the formation of the initial diploid species in the Cynodon genus.
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Affiliation(s)
- Shuhao Yu
- Department of Horticulture and Landscape Architecture, Oklahoma State University, 358 Agriculture Hall, Stillwater, OK 74078, USA
| | - Hongxu Dong
- Department of Plant and Soil Sciences, Mississippi State University, 358 Dorman Hall, Mississippi State, MS 39762, USA
| | - Tilin Fang
- Department of Plant and Soil Sciences, Oklahoma State University, 371 Agriculture Hall, Stillwater, OK 74078, USA
| | - Yanqi Wu
- Department of Horticulture and Landscape Architecture, Oklahoma State University, 358 Agriculture Hall, Stillwater, OK 74078, USA
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Levy AA, Feldman M. Evolution and origin of bread wheat. THE PLANT CELL 2022; 34:2549-2567. [PMID: 35512194 PMCID: PMC9252504 DOI: 10.1093/plcell/koac130] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
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20
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Moreno-Aguilar MF, Inda LA, Sánchez-Rodríguez A, Arnelas I, Catalán P. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. FRONTIERS IN PLANT SCIENCE 2022; 13:901733. [PMID: 35845705 PMCID: PMC9284676 DOI: 10.3389/fpls.2022.901733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
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Affiliation(s)
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Instituto Agroalimentario de Aragón, Universidad de Zaragoza, Centro de Investigación y Tecnología Agroalimentaria, Zaragoza, Spain
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Itziar Arnelas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Unidad Asociada al CSIC, Zaragoza, Spain
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21
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Sharma H, Batra R, Kumar S, Kumar M, Kumar S, Balyan HS, Gupta PK. Identification and characterization of 20S proteasome genes and their relevance to heat/drought tolerance in bread wheat. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Zhang S, Xia Z, Li C, Wang X, Lu X, Zhang W, Ma H, Zhou X, Zhang W, Zhu T, Liu P, Liu G, Wang W, Xia T. Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureum Schum.). Mol Ecol Resour 2022; 22:2363-2378. [PMID: 35347881 DOI: 10.1111/1755-0998.13612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 11/29/2022]
Abstract
Elephant grass (Pennisetum purpureum Schum) is an important forage, biofuels and industrial plant widely distributed in tropical and subtropical areas globally. It is characterized with robust growth and high biomass. We sequenced its allopolyploid genome and assembled 2.07 Gb into A' and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb, yielding a total of 77,139 genes. The allotetraploid speciation occurred approximately 15 MYA after the divergence between Setaria italica and Pennisetum glaucum, according to a phylogenetic analysis of Pennisetum species. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional divergence between sub-genomes A' and B. A' sub-genome mainly contributed to plant growth, development and photosynthesis, whereas the B sub-genome was primarily responsible for effective transportation and resistance to stimulation. Some key gene families related to cellulose biosynthesis were expanded and highly expressed in stems, which could explain the high cellulose content in elephant grass. Our findings provide deep insights into genetic evolution of elephant grass and will aid future biological research and breeding, even for other grasses in the family Poaceae.
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Affiliation(s)
- Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Zhiqiang Xia
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China
| | - Can Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xiaohan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xianqin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Wenqing Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Haizhen Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Weixiong Zhang
- Department of Computer Science and Engineering, Department of Genetics, Washington University, St. Louis, MO, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Pandao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Guodao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
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23
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Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE ( SPL) Gene Family between Wheat and Rice. Int J Mol Sci 2022; 23:ijms23042099. [PMID: 35216210 PMCID: PMC8874652 DOI: 10.3390/ijms23042099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022] Open
Abstract
The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs’ functions in rice to facilitate the functional genomics of TaSPL genes. To achieve these goals, we combined several approaches, including genome-wide analysis of TaSPLs, comparative genomic analysis, expression profiling, and functional study of TaSPL3 in rice. We established the orthologous relationships of 56 TaSPL genes with the corresponding OsSPLs, laying a foundation for the comparison of known SPL functions between wheat and rice. Some TaSPLs exhibited different spatial–temporal expression patterns when compared to their rice orthologs, thus implicating functional divergence. TaSPL2/6/8/10 were identified to respond to different abiotic stresses through the combination of RNA-seq and qPCR expression analysis. Additionally, ectopic expression of TaSPL3 in rice promotes heading dates, affects leaf and stem development, and leads to smaller panicles and decreased yields per panicle. In conclusion, our work provides useful information toward cataloging of the functions of TaSPLs, emphasized the conservation and divergence between TaSPLs and OsSPLs, and identified the important SPL genes for wheat improvement.
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Yu L, Ma S, Zhang X, Tian D, Yang S, Jia X, Traw MB. Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1365-1381. [PMID: 34585814 DOI: 10.1111/tpj.15516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.
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Affiliation(s)
- Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shiying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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25
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Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Streptochaeta Genome and the Evolution of the Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:710383. [PMID: 34671369 PMCID: PMC8521107 DOI: 10.3389/fpls.2021.710383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/08/2021] [Indexed: 05/15/2023]
Abstract
In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
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Affiliation(s)
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | | | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Wang J, Zi H, Wang R, Liu J, Wang H, Chen R, Li L, Guo H, Chen J, Li J, Zong J. A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit. HORTICULTURE RESEARCH 2021; 8:201. [PMID: 34465733 PMCID: PMC8408263 DOI: 10.1038/s41438-021-00636-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 05/15/2023]
Abstract
Centipedegrass [Eremochloa ophiuroides (Munro) Hack.], a member of the Panicoideae subfamily, is one of the most important warm-season turfgrasses originating from China. This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions. To better understand the genetic basis of important biological characteristics, such as prostrate growth and seed yield, in warm-season turfgrasses, we present a high-quality reference genome for centipedegrass and use PacBio, BioNano, and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes, with a scaffold N50 of 86.05 Mb and 36,572 annotated genes. Centipedegrass was most closely related to sorghum and diverged from their common ancestor ~16.8 Mya. We detected a novel chromosome reshuffling event in centipedegrass, namely, the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum. The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1 (PROG1) genes on chromosome 2. Two orthologous genes of OsPROG1, EoPROG1, and EoPROG2, were confirmed to increase the stem number and decrease the stem angle in Arabidopsis. Collectively, our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.
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Affiliation(s)
- Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing, China
| | - Rui Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Rongrong Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
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27
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Haas M, Kono T, Macchietto M, Millas R, McGilp L, Shao M, Duquette J, Qiu Y, Hirsch CN, Kimball J. Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1802-1818. [PMID: 34310794 DOI: 10.1111/tpj.15419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.
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Affiliation(s)
- Matthew Haas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa Macchietto
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Reneth Millas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mingqin Shao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jacques Duquette
- North Central Research and Outreach Center, University of Minnesota, Grand Rapids, MN, 55744, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jennifer Kimball
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
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28
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Shen C, Yuan J, Ou X, Ren X, Li X. Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat ( Triticum aestivum). PeerJ 2021; 9:e11861. [PMID: 34386306 PMCID: PMC8312495 DOI: 10.7717/peerj.11861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear. Methods A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication. Results The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingqi Ou
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiujuan Ren
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xinhua Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
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Schreier TB, Fahy B, David LC, Siddiqui H, Castells-Graells R, Smith AM. Introduction of glucan synthase into the cytosol in wheat endosperm causes massive maltose accumulation and represses starch synthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1431-1442. [PMID: 33764607 DOI: 10.1111/tpj.15246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
We expressed a bacterial glucan synthase (Agrobacterium GlgA) in the cytosol of developing endosperm cells in wheat grains, to discover whether it could generate a glucan from cytosolic ADP-glucose. Transgenic lines had high glucan synthase activity during grain filling, but did not accumulate glucan. Instead, grains accumulated very high concentrations of maltose. They had large volumes during development due to high water content, and very shrivelled grains at maturity. Starch synthesis was severely reduced. We propose that cytosolic glucan synthesized by the glucan synthase was immediately hydrolysed to maltose by cytosolic β-amylase(s). Maltose accumulation resulted in a high osmotic potential in developing grain, drawing in excess water that stretched the seed coat and pericarp. Loss of water during grain maturation then led to shrinkage when the grains matured. Maltose accumulation is likely to account for the reduced starch synthesis in transgenic grains, through signalling and toxic effects. Using bioinformatics, we identify an isoform of β-amylase likely to be responsible for maltose accumulation. Removal of this isoform through identification of TILLING mutants or genome editing, combined with co-expression of heterologous glucan synthase and a glucan branching enzyme, may in future enable elevated yields of carbohydrate through simultaneous accumulation of starch and cytosolic glucan.
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Affiliation(s)
- Tina B Schreier
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing St, Cambridge, CB2 3EA, UK
| | - Brendan Fahy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Laure C David
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- ETH Department of Biology, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Hamad Siddiqui
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Germains Seed Technology, Lab 7, Centrum, Norwich Research Park, Norwich, NR4 7UG, UK
| | - Roger Castells-Graells
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Alison M Smith
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Ma PF, Liu YL, Jin GH, Liu JX, Wu H, He J, Guo ZH, Li DZ. The Pharus latifolius genome bridges the gap of early grass evolution. THE PLANT CELL 2021; 33:846-864. [PMID: 33630094 PMCID: PMC8226297 DOI: 10.1093/plcell/koab015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/11/2021] [Indexed: 05/07/2023]
Abstract
The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a grass species (producing a true spikelet) in the subfamily Pharoideae, a sister lineage to the core Poaceae including the (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) and Bambusoideae, Oryzoideae, and Pooideae (BOP) clades. Our results indicate that the P. latifolius genome has evolved slowly relative to cereal grass genomes, as reflected by moderate rates of molecular evolution, limited chromosome rearrangements and a low rate of gene loss for duplicated genes. We show that the ρ-WGD event occurred approximately 98.2 million years ago (Ma) in a common ancestor of the Pharoideae and the PACMAD and BOP grasses. This was followed by contrasting patterns of diploidization in the Pharus and core Poaceae lineages. The presence of two FRIZZY PANICLE-like genes in P. latifolius, and duplicated MADS-box genes, support the hypothesis that the ρ-WGD may have played a role in the origin and functional diversification of the spikelet, an adaptation in grasses related directly to cereal yields. The P. latifolius genome sheds light on the origin and early evolution of grasses underpinning the biology and breeding of cereals.
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Affiliation(s)
- Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Gui-Hua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China
| | - Jun He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, China
- Author for correspondence: (D.-Z.L)
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31
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Wang C, Wang T, Yin M, Eller F, Liu L, Brix H, Guo W. Transcriptome Analysis of Tetraploid and Octoploid Common Reed ( Phragmites australis). FRONTIERS IN PLANT SCIENCE 2021; 12:653183. [PMID: 34025698 PMCID: PMC8132968 DOI: 10.3389/fpls.2021.653183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Polyploidization in plants is thought to have occurred as coping mechanism with environmental stresses. Polyploidization-driven adaptation is often achieved through interplay of gene networks involved in differentially expressed genes, which triggers the plant to evolve special phenotypic traits for survival. Phragmites australis is a cosmopolitan species with highly variable phenotypic traits and high adaptation capacity to various habitats. The species' ploidy level varies from 3x to 12x, thus it is an ideal organism to investigate the molecular evolution of polyploidy and gene regulation mediated by different numbers of chromosome copies. In this study, we used high-throughput RNAseq data as a tool, to analyze the gene expression profiles in tetraploid and octoploid P. australis. The estimated divergence time between tetraploid and octoploid P. australis was dated to the border between Pliocene and Pleistocene. This study identified 439 up- and 956 down-regulated transcripts in tetraploids compared to octoploids. Gene ontology and pathway analysis revealed that tetraploids tended to express genes responsible for reproduction and seed germination to complete the reproduction cycle early, and expressed genes related to defense against UV-B light and fungi, whereas octoploids expressed mainly genes related to thermotolerance. Most differentially expressed genes were enriched in chaperones, folding catalysts and protein processing in endoplasmic reticulum pathways. Multiple biased isoform usage of the same gene was detected in differentially expressed genes, and the ones upregulated in octoploids were related to reduced DNA methylation. Our study provides new insights into the role of polyploidization on environmental responses and potential stress tolerance in grass species.
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Affiliation(s)
- Cui Wang
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tong Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Meiqi Yin
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
| | | | - Lele Liu
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
| | - Hans Brix
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Weihua Guo
- Institute of Ecology and Biodiversity, Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, School of Life Sciences, Shandong University, Qingdao, China
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32
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The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress. Int J Mol Sci 2021; 22:ijms22063111. [PMID: 33803701 PMCID: PMC8002965 DOI: 10.3390/ijms22063111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
FBX proteins are subunits of the SCF complex (Skp1-cullin-FBX) belonging to the E3 ligase family, which is involved in the ubiquitin-proteasome 26S (UPS) pathway responsible for the post-translational protein turnover. By targeting, in a selective manner, key regulatory proteins for ubiquitination and 26S proteasome degradation, FBX proteins play a major role in plant responses to diverse developmental and stress conditions. Although studies on the genomic organization of the FBX gene family in various species have been reported, knowledge related to bread wheat (Triticum aestivum) is scarce and needs to be broadened. Using the latest assembly of the wheat genome, we identified 3670 TaFBX genes distributed non-homogeneously within the three subgenomes (A, B and D) and between the 21 chromosomes, establishing it as one of the richest gene families among plant species. Based on the presence of the five different chromosomal regions previously identified, the present study focused on the genomic distribution of the TaFBX family and the identification of differentially expressed genes during the embryogenesis stages and in response to heat and drought stress. Most of the time, when comparing the expected number of genes (taking into account the formal gene distribution on the entire wheat genome), the TaFBX family harbors a different pattern at the various stratum of observation (subgenome, chromosome, chromosomal regions). We report here that the local gene expansion of the TaFBX family must be the consequence of multiple and complex events, including tandem and small-scale duplications. Regarding the differentially expressed TaFBX genes, while the majority of the genes are localized in the distal chromosomal regions (R1 and R3), differentially expressed genes are more present in the interstitial regions (R2a and R2b) than expected, which could be an indication of the preservation of major genes in those specific chromosomal regions.
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34
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Siddiqui MN, Léon J, Naz AA, Ballvora A. Genetics and genomics of root system variation in adaptation to drought stress in cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1007-1019. [PMID: 33096558 PMCID: PMC7904151 DOI: 10.1093/jxb/eraa487] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Ali A Naz
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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35
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Li G, Wang L, Yang J, He H, Jin H, Li X, Ren T, Ren Z, Li F, Han X, Zhao X, Dong L, Li Y, Song Z, Yan Z, Zheng N, Shi C, Wang Z, Yang S, Xiong Z, Zhang M, Sun G, Zheng X, Gou M, Ji C, Du J, Zheng H, Doležel J, Deng XW, Stein N, Yang Q, Zhang K, Wang D. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nat Genet 2021; 53:574-584. [PMID: 33737755 PMCID: PMC8035075 DOI: 10.1038/s41588-021-00808-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
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Affiliation(s)
- Guangwei Li
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Lijian Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Jianping Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Hang He
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Huaibing Jin
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xuming Li
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Tianheng Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Zhenglong Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Feng Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xue Han
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiaoge Zhao
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lingli Dong
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhongping Song
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zehong Yan
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Nannan Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Cuilan Shi
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zhaohui Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Shuling Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zijun Xiong
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Menglan Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Guanghua Sun
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xu Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Mingyue Gou
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Changmian Ji
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Junkai Du
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Hongkun Zheng
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Jaroslav Doležel
- grid.454748.eInstitute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Xing Wang Deng
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Qinghua Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Kunpu Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
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36
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Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB. CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1301-1314. [PMID: 32996244 DOI: 10.1111/tpj.15001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 05/07/2023]
Abstract
Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - M Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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37
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Zhao N, Dong Q, Nadon BD, Ding X, Wang X, Dong Y, Liu B, Jackson SA, Xu C. Evolution of Homeologous Gene Expression in Polyploid Wheat. Genes (Basel) 2020; 11:genes11121401. [PMID: 33255795 PMCID: PMC7759873 DOI: 10.3390/genes11121401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/16/2020] [Accepted: 11/21/2020] [Indexed: 11/17/2022] Open
Abstract
Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.
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Affiliation(s)
- Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China;
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA;
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Q.D.); (X.W.); (Y.D.); (B.L.)
| | - Brian D. Nadon
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA;
| | - Xiaoyang Ding
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China;
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Q.D.); (X.W.); (Y.D.); (B.L.)
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Q.D.); (X.W.); (Y.D.); (B.L.)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Q.D.); (X.W.); (Y.D.); (B.L.)
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA;
- Bayer Crop Science, Chesterfield, MO 63017, USA
- Correspondence: or (S.A.J.); (C.X.); Tel.: +86-0431-8509-9367 (C.X.)
| | - Chunming Xu
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA;
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Q.D.); (X.W.); (Y.D.); (B.L.)
- Correspondence: or (S.A.J.); (C.X.); Tel.: +86-0431-8509-9367 (C.X.)
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Lim SD, Oh DG, Park YC, Jang CS. Molecular characterization of a RING E3 ligase SbHCI1 in sorghum under heat and abscisic acid stress. PLANTA 2020; 252:89. [PMID: 33064214 DOI: 10.1007/s00425-020-03469-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/12/2020] [Indexed: 05/16/2023]
Abstract
Molecular function ofRING E3 ligase SbHCI1is involved in ABA-mediated basal heat stress tolerancein sorghum. Global warming generally reduces plant survival, owing to the negative effects of high temperatures on plant development. However, little is known about the role of Really Interesting New Gene (RING) E3 ligase in the heat stress responses of plants. As such, the aim of the present study was to characterize the molecular functions of the Sorghum bicolor ortholog of the Oryza sativa gene for Heat- and Cold-Induced RING finger protein 1 (SbHCI1). Subcellular localization revealed that SbHCI1 was mainly associated with the cytosol and that it moved to the Golgi apparatus under heat stress conditions. The fluorescent signals of SbHCI1 substrate proteins were observed to migrate to the cytoplasm under heat stress conditions. Bimolecular fluorescence complementation (BiFC) and yeast two-hybrid (Y2H) assays revealed that SbHCI1 physically interacted with OsHCI1 ortholog partner proteins in the cytoplasm. Moreover, an in vitro ubiquitination assay revealed that SbHCI1 polyubiquitinated each of the three interacting proteins. The ectopic overexpression of SbHCI1 in Arabidopsis revealed that the protein was capable of inducing abscisic acid (ABA)-hypersensitivity and basal heat stress tolerance. Therefore, SbHCI1 possesses E3 ligase activity and may function as a positive regulator of heat stress responses through the modulation of interacting proteins.
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Affiliation(s)
- Sung Don Lim
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Dae Gyeom Oh
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Yong Chan Park
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5808-5822. [PMID: 32725154 DOI: 10.1093/jxb/eraa355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Chuan Ge
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Wenyun Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Linyi Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Bretani G, Rossini L, Ferrandi C, Russell J, Waugh R, Kilian B, Bagnaresi P, Cattivelli L, Fricano A. Segmental duplications are hot spots of copy number variants affecting barley gene content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1073-1088. [PMID: 32338390 PMCID: PMC7496488 DOI: 10.1111/tpj.14784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 05/31/2023]
Abstract
Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.
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Affiliation(s)
- Gianluca Bretani
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Chiara Ferrandi
- Parco Tecnologico PadanoLoc. C.na CodazzaVia Einstein26900LodiItaly
| | | | - Robbie Waugh
- James Hutton Institute, InvergowrieDundeeDD2 5DAUK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 306466GaterslebenGermany
- Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
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Jiang W, Yin J, Zhang H, He Y, Shuai S, Chen S, Cao S, Li W, Ma D, Chen H. Genome-wide identification, characterization analysis and expression profiling of auxin-responsive GH3 family genes in wheat (Triticum aestivum L.). Mol Biol Rep 2020; 47:3885-3907. [DOI: 10.1007/s11033-020-05477-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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Rubert DP, Martinez FV, Stoye J, Doerr D. Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. BMC Genomics 2020; 21:273. [PMID: 32299356 PMCID: PMC7160886 DOI: 10.1186/s12864-020-6609-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. RESULTS Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants. CONCLUSIONS Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept.
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Affiliation(s)
- Diego P. Rubert
- Faculdade de Computação – FACOM, Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Fábio V. Martinez
- Faculdade de Computação – FACOM, Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Daniel Doerr
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivars. Sci Rep 2019; 9:19362. [PMID: 31852940 PMCID: PMC6920420 DOI: 10.1038/s41598-019-55652-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. Its highly polyploid, complex genome has hindered progress in understanding its molecular structure. Flow cytometric sorting and analysis has been used in other important crops with large genomes to dissect the genome into component chromosomes. Here we present for the first time a method to prepare suspensions of intact sugarcane chromosomes for flow cytometric analysis and sorting. Flow karyotypes were generated for two S. officinarum and three hybrid cultivars. Five main peaks were identified and each genotype had a distinct flow karyotype profile. The flow karyotypes of S. officinarum were sharper and with more discrete peaks than the hybrids, this difference is probably due to the double genome structure of the hybrids. Simple Sequence Repeat (SSR) markers were used to determine that at least one allelic copy of each of the 10 basic chromosomes could be found in each peak for every genotype, except R570, suggesting that the peaks may represent ancestral Saccharum sub genomes. The ability to flow sort Saccharum chromosomes will allow us to isolate and analyse chromosomes of interest and further examine the structure and evolution of the sugarcane genome.
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Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.). BMC Genomics 2019; 20:986. [PMID: 31842737 PMCID: PMC6916456 DOI: 10.1186/s12864-019-6374-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. RESULTS A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. CONCLUSIONS In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.
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45
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Park YC, Choi SY, Kim JH, Jang CS. Molecular Functions of Rice Cytosol-Localized RING Finger Protein 1 in Response to Salt and Drought and Comparative Analysis of Its Grass Orthologs. PLANT & CELL PHYSIOLOGY 2019; 60:2394-2409. [PMID: 31292649 DOI: 10.1093/pcp/pcz133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/02/2019] [Indexed: 05/29/2023]
Abstract
In higher plants, the post-translational modification of target proteins via the attachment of molecules such as ubiquitin (Ub) mediates a variety of cellular functions via the Ub/26S proteasome system. Here, a really interesting new gene (RING)-H2 type E3 ligase, which regulates target proteins via the Ub/26S proteasome system, was isolated from a rice plant, and its other grass orthologs were examined to determine the evolution of its molecular function during speciation. The gene encoding Oryza sativa cytoplasmic-localized RING finger protein 1 (OsCLR1) was highly expressed under salt and drought stresses. By contrast, the three grass orthologs, SbCLR1 from Sorghum bicolor, ZmCLR1 from Zea mays and TaCLR1 from Triticum aestivum, showed different responses to these stresses. Despite these differences, all four orthologs exhibited E3 ligase activity with cytosol-targeted localization, demonstrating conserved molecular functions. Although OsCLR1-overexpressing plants showed higher survival rates under both salt and drought stresses than that of the wild type (WT) plants, this pattern was not observed in the other orthologs. In addition, OsCLR1-overexpressing plants exhibited lower germination rates in ABA than that of WT plants, whereas the three ortholog CLR1-overexpressing plants showed rates similar to the WT plants. These results indicate the positive regulation of OsCLR1 in response to salt and drought in an ABA-dependent manner. Despite the molecular functions of the three CLR1 orthologs remaining largely unknown, our results provide an insight into the evolutionary fate of CLR1 grass orthologs during speciation after the divergence from a common ancestor.
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Affiliation(s)
- Yong Chan Park
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Seung Young Choi
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Jong Ho Kim
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, Republic of Korea
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46
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Beauclair L, Ramé C, Arensburger P, Piégu B, Guillou F, Dupont J, Bigot Y. Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies. BMC Genomics 2019; 20:734. [PMID: 31610792 PMCID: PMC6792250 DOI: 10.1186/s12864-019-6131-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Background More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian genomes often contain sequences with high GC content, which has been hypothesized to be at the origin of many missing sequences in these genomes. We investigated features of these missing sequences to discover why some may not have been integrated into genomic libraries and/or sequenced. Results The sequences of five red jungle fowl cDNA models with high GC content were used as queries to search publicly available datasets of Illumina and Pacbio sequencing reads. These were used to reconstruct the leptin, TNFα, MRPL52, PCP2 and PET100 genes, all of which are absent from the red jungle fowl genome model. These gene sequences displayed elevated GC contents, had intron sizes that were sometimes larger than non-avian orthologues, and had non-coding regions that contained numerous tandem and inverted repeat sequences with motifs able to assemble into stable G-quadruplexes and intrastrand dyadic structures. Our results suggest that Illumina technology was unable to sequence the non-coding regions of these genes. On the other hand, PacBio technology was able to sequence these regions, but with dramatically lower efficiency than would typically be expected. Conclusions High GC content was not the principal reason why numerous GC-rich regions of avian genomes are missing from genome assembly models. Instead, it is the presence of tandem repeats containing motifs capable of assembling into very stable secondary structures that is likely responsible.
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Affiliation(s)
- Linda Beauclair
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Christelle Ramé
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, 91768, USA
| | - Benoît Piégu
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Florian Guillou
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Joëlle Dupont
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France
| | - Yves Bigot
- PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de Loire, 37380, Nouzilly, France.
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Peng X, Wang Q, Zhao Y, Li X, Ma Q. Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. Genet Mol Biol 2019; 42:380-394. [PMID: 31271590 PMCID: PMC6726161 DOI: 10.1590/1678-4685-gmb-2017-0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2018] [Indexed: 11/21/2022] Open
Abstract
SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis, rice, and Populus. However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six groups according to phylogeny. We found that most of the SPL-containing regions in maize showed extensive conservation with duplicated regions of rice and sorghum. A gene duplication analysis in maize indicated that ZmSPLs showed a significant excess of segmental duplication. The Ka/Ks analysis indicated that 9 out of 18 duplicated pairs in maize experienced positive selection, while SPL gene pairs of rice and sorghum mainly evolved under purifying selection, suggesting novel evolutionary features for ZmSPLs. The 31 ZmSPLs were further analyzed by describing their gene structure, phylogenetic relationships, chromosomal location, and expression, Among the ZmSPLs, 13 were predicated to be targeted by miR156s and involved in drought stress response. These results provide the foundation for future functional analyses of ZmSPLs.
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Affiliation(s)
- Xiaojian Peng
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qianqian Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance, Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
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Fan G, Zhang Y, Liu X, Wang J, Sun Z, Sun S, Zhang H, Chen J, Lv M, Han K, Tan X, Hu J, Guan R, Fu Y, Liu S, Chen X, Xu Q, Qin Y, Liu L, Bai J, Wang O, Tang J, Lu H, Shang Z, Wang B, Hu G, Zhao X, Zou Y, Chen A, Gong M, Zhang W, Lee SM, Li S, Liu J, Li Z, Lu Y, Sabir JSM, Sabir MJ, Khan M, Hajrah NH, Yin Y, Kristiansen K, Yang H, Wang J, Xu X, Liu X. The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution. Mol Ecol Resour 2019; 19:944-956. [DOI: 10.1111/1755-0998.13003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
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New insights into the origin and evolution of α-amylase genes in green plants. Sci Rep 2019; 9:4929. [PMID: 30894656 PMCID: PMC6426938 DOI: 10.1038/s41598-019-41420-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/05/2018] [Indexed: 01/16/2023] Open
Abstract
Gene duplication is a source of genetic materials and evolutionary changes, and has been associated with gene family expansion. Functional divergence of duplicated genes is strongly directed by natural selections such as organism diversification and novel feature acquisition. We show that, plant α-amylase gene family (AMY) is comprised of six subfamilies (AMY1-AMY6) that fell into two ancient phylogenetic lineages (AMY3 and AMY4). Both AMY1 and AMY2 are grass-specific and share a single-copy ancestor, which is derived from grass AMY3 genes that have undergone massive tandem and whole-genome duplications during evolution. Ancestral features of AMY4 and AMY5/AMY6 genes have been retained among four green algal sequences (Chrein_08.g362450, Vocart_0021s0194, Dusali_0430s00012 and Monegl_16464), suggesting a gene duplication event following Chlorophyceae diversification. The observed horizontal gene transfers between plant and bacterial AMYs, and chromosomal locations of AMY3 and AMY4 genes in the most ancestral green body (C. reinhardtii), provide evidences for the monophyletic origin of plant AMYs. Despite subfamily-specific sequence divergence driven by natural selections, the active site and SBS1 are well-conserved across different AMY isoforms. The differentiated electrostatic potentials and hydrogen bands-forming residue polymorphisms, further imply variable digestive abilities for a broad substrates in particular tissues or subcellular localizations.
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50
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Batra R, Agarwal P, Tyagi S, Saini DK, Kumar V, Kumar A, Kumar S, Balyan HS, Pandey R, Gupta PK. A study of CCD8 genes/proteins in seven monocots and eight dicots. PLoS One 2019; 14:e0213531. [PMID: 30861026 PMCID: PMC6413960 DOI: 10.1371/journal.pone.0213531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/23/2019] [Indexed: 02/08/2023] Open
Abstract
In plants, the enzyme CCD8 (carotenoid cleavage dioxygenase 8) is involved in the synthesis of an important hormone, strigolactone, and therefore, plays an important role in controlling growth and development. Using cDNA and protein sequence derived from the gene ZmCCD8 from maize, we identified putative orthologs of the gene encoding CCD8 in six other monocots and eight dicots; the sequence similarity ranged from 52–75.9% at the gene level and 60.9–93.7% at the protein level. The average length of the gene was ~3.3 kb (range: 2.08 to 3.98 kb), although the number of introns within the genes differed (4 or 5 in dicots and 3 or 4 in monocots, except in T. urartu with 6 introns). Several cis-acting regulatory elements were identified in the promoters of CCD8 genes, which are known to respond to biotic and abiotic stresses. The N-terminal end (up to ~70 amino acids) of CCD8 proteins was highly variable due to insertions, deletions and mismatches. The variation in genes and proteins were particularly conspicuous in T. urartu and Ae. tauschii among the monocots and A. thaliana and P. persica among the dicots. In CCD8 proteins, 12 motifs were also identified, of which 6 were novel; 4 of these novel motifs occurred in all the 15 species. The 3D structures of proteins had the characteristic features of the related enzyme apocarotenoid oxygenase (ACO) of Synechocystis (a representative of cyanobacteria). The results of qRT-PCR in wheat revealed that under phosphorous (P)-starved condition (relative to expression under optimum P used as control), the expression of TaCCD8 genes increased ~37 fold in root tissue of the cultivar C306 and ~33 fold in shoot tissue of the cultivar HUW468 (the two cultivars differed in their P-use efficiency). This suggested that expression of TaCCD8 genes is genotype-dependent and tissue-specific and is regulated under different levels of P supply.
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Affiliation(s)
- Ritu Batra
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Sandhya Tyagi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Kumar Saini
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Vikas Kumar
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - Sanjay Kumar
- Bioinformatics Centre, Biotech Park, Lucknow, India
| | | | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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