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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Mishra A, Dash S, Barpanda T, Choudhury S, Mishra P, Dash M, Swain D. Improvement of little millet (Panicum sumatrense) using novel omics platform and genetic resource integration. PLANTA 2024; 260:60. [PMID: 39052093 DOI: 10.1007/s00425-024-04493-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
MAIN CONCLUSION This article explores possible future initiatives, such as the development of targeted breeding and integrated omics approach to boost little millet production, nutritional value, and environmental adaptation. Little millet (P. sumatrense) is a staple grain in many parts of Asia and Africa owing to its abundance in vitamins and minerals and its ability to withstand harsh agro-ecological conditions. Enhancing little millet using natural resources and novel crop improvement strategy is an effective way of boosting nutritional and food security. To understand the genetic makeup of the crop and figure out important characteristics linked to nutritional value, biotic and abiotic resistance, and production, researchers in this field are currently resorting on genomic technology. These realizations have expedited the crop's response to shifting environmental conditions by enabling the production of superior cultivars through targeted breeding. Going forward, further improvements in breeding techniques and genetics may boost the resilience, nutritional content, and production of little millet, which would benefit growers and consumers alike. The research and development on little millet improvement using novel omics platform and the integration of genetic resources are summarized in this review paper. Improved cultivars of little millet that satisfy changing farmer and consumer demands have already been developed through the use of these novel breeding strategies. This article also explores possible future initiatives, such as the development of targeted breeding, genomics, and sustainable agriculture methods. The potential for these measures to boost little millet's overall production, nutritional value, and climate adaptation will be extremely helpful in addressing nutritional security.
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Affiliation(s)
- Abinash Mishra
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.
| | - Suman Dash
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Tanya Barpanda
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Suman Choudhury
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Pratikshya Mishra
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Manasi Dash
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Digbijaya Swain
- Department of Genetics and Plant Breeding, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
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3
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Liu F, Baye W, Zhao K, Tang S, Xie Q, Xie P. Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. J Genet Genomics 2024:S1673-8527(24)00194-2. [PMID: 39053846 DOI: 10.1016/j.jgg.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.
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Affiliation(s)
- Fangyuan Liu
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wodajo Baye
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Natural and Computational Science, Woldia University, Woldia, Po.box-400, Ethiopia.
| | - Kangxu Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Xie
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 PMCID: PMC11237005 DOI: 10.1038/s42003-024-06525-7] [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: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Chen X, He C, Xu H, Zeng G, Huang Q, Deng Z, Qin X, Shen X, Hu Y. Characterization of the SWI/SNF complex and nucleosome organization in sorghum. FRONTIERS IN PLANT SCIENCE 2024; 15:1430467. [PMID: 38988640 PMCID: PMC11234113 DOI: 10.3389/fpls.2024.1430467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024]
Abstract
The switch defective/sucrose non-fermentable (SWI/SNF) multisubunit complex plays an important role in the regulation of gene expression by remodeling chromatin structure. Three SWI/SNF complexes have been identified in Arabidopsis including BAS, SAS, and MAS. Many subunits of these complexes are involved in controlling plant development and stress response. However, the function of these complexes has hardly been studied in other plant species. In this study, we identified the subunits of the SWI/SNF complex in sorghum and analyzed their evolutionary relationships in six grass species. The grass species conserved all the subunits as in Arabidopsis, but gene duplication occurred diversely in different species. Expression pattern analysis in sorghum (Sorghum bicolor) showed that most of the subunit-encoding genes were expressed constitutively, although the expression level was different. Transactivation assays revealed that SbAN3, SbGIF3, and SbSWI3B possessed transactivation activity, which suggests that they may interact with the pre-initiation complex (PIC) to activate transcription. We chose 12 subunits in sorghum to investigate their interaction relationship by yeast two-hybrid assay. We found that these subunits displayed distinct interaction patterns compared to their homologs in Arabidopsis and rice. This suggests that different SWI/SNF complexes may be formed in sorghum to perform chromatin remodeling functions. Through the integrated analysis of MNase-seq and RNA-seq data, we uncovered a positive relationship between gene expression levels and nucleosome phasing. Furthermore, we found differential global nucleosome enrichments between leaves and roots, as well as in response to PEG treatment, suggesting that dynamics of nucleosome occupancy, which is probably mediated by the SWI/SNF complex, may play important roles in sorghum development and stress response.
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Affiliation(s)
- Xiaofei Chen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Huan Xu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Gongjian Zeng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Quanjun Huang
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Zhuying Deng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xiner Qin
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xiangling Shen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yongfeng Hu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
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6
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Agnew E, Ziegler G, Lee S, Lizárraga C, Fahlgren N, Baxter I, Mockler TC, Shakoor N. Longitudinal genome-wide association study reveals early QTL that predict biomass accumulation under cold stress in sorghum. FRONTIERS IN PLANT SCIENCE 2024; 15:1278802. [PMID: 38807776 PMCID: PMC11130433 DOI: 10.3389/fpls.2024.1278802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Introduction Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy due to its high biomass yields. However, early growth phases of sorghum are sensitive to cold stress, limiting its planting in temperate environments. Cold adaptability is crucial for cultivating bioenergy and grain sorghum at higher latitudes and elevations, or for extending the growing season. Identifying genes and alleles that enhance biomass accumulation under early cold stress can lead to improved sorghum varieties through breeding or genetic engineering. Methods We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP includes diverse accessions with dense genotyping and varied racial, geographical, and phenotypic backgrounds. Daily, non-destructive imaging allowed temporal analysis of growth-related traits and water use efficiency (WUE). A genome-wide association study (GWAS) was performed to identify genomic intervals and genes associated with cold stress response. Results The GWAS identified transient quantitative trait loci (QTL) strongly associated with growth-related traits, enabling an exploration of the genetic basis of cold stress response at different developmental stages. This analysis of daily growth traits, rather than endpoint traits, revealed early transient QTL predictive of final phenotypes. The study identified both known and novel candidate genes associated with growth-related traits and temporal responses to cold stress. Discussion The identified QTL and candidate genes contribute to understanding the genetic mechanisms underlying sorghum's response to cold stress. These findings can inform breeding and genetic engineering strategies to develop sorghum varieties with improved biomass yields and resilience to cold, facilitating earlier planting, extended growing seasons, and cultivation at higher latitudes and elevations.
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Affiliation(s)
| | | | | | | | | | | | | | - Nadia Shakoor
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
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7
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El-Azaz J, Moore B, Takeda-Kimura Y, Yokoyama R, Wijesingha Ahchige M, Chen X, Schneider M, Maeda HA. Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses. Nat Commun 2023; 14:7242. [PMID: 37945591 PMCID: PMC10636026 DOI: 10.1038/s41467-023-42587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
Vascular plants direct large amounts of carbon to produce the aromatic amino acid phenylalanine to support the production of lignin and other phenylpropanoids. Uniquely, grasses, which include many major crops, can synthesize lignin and phenylpropanoids from both phenylalanine and tyrosine. However, how grasses regulate aromatic amino acid biosynthesis to feed this dual lignin pathway is unknown. Here we show, by stable-isotope labeling, that grasses produce tyrosine >10-times faster than Arabidopsis without compromising phenylalanine biosynthesis. Detailed in vitro enzyme characterization and combinatorial in planta expression uncovered that coordinated expression of specific enzyme isoforms at the entry and exit steps of the aromatic amino acid pathway enables grasses to maintain high production of both tyrosine and phenylalanine, the precursors of the dual lignin pathway. These findings highlight the complex regulation of plant aromatic amino acid biosynthesis and provide novel genetic tools to engineer the interface of primary and specialized metabolism in plants.
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Affiliation(s)
- Jorge El-Azaz
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Bethany Moore
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Yuri Takeda-Kimura
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Faculty of Agriculture, Yamagata University, Yamagata-shi, Japan
| | - Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Micha Wijesingha Ahchige
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Xuan Chen
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- International Institute of Tea Industry Innovation for "one Belt, one Road", Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Matthew Schneider
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Cell Culture Company, Minneapolis, MN, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Chemelewski R, McKinley BA, Finlayson S, Mullet JE. Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development. FRONTIERS IN PLANT SCIENCE 2023; 14:1227859. [PMID: 37936930 PMCID: PMC10626490 DOI: 10.3389/fpls.2023.1227859] [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: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 11/09/2023]
Abstract
Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum's resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm2) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.
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Affiliation(s)
- Robert Chemelewski
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Brian A. McKinley
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Scott Finlayson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - John E. Mullet
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
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Yang L, Zhou Q, Sheng X, Chen X, Hua Y, Lin S, Luo Q, Yu B, Shao T, Wu Y, Chang J, Li Y, Tu M. Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications. Int J Mol Sci 2023; 24:14549. [PMID: 37833996 PMCID: PMC10573072 DOI: 10.3390/ijms241914549] [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: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.
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Affiliation(s)
- Lin Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qin Zhou
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Xuan Sheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiangqian Chen
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Yuqing Hua
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Shuang Lin
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qiyun Luo
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Boju Yu
- 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; (B.Y.); (T.S.); (J.C.)
| | - Ti Shao
- 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; (B.Y.); (T.S.); (J.C.)
| | - Yixiao Wu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - 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; (B.Y.); (T.S.); (J.C.)
| | - 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; (B.Y.); (T.S.); (J.C.)
| | - Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
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10
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Yoda A, Xie X, Yoneyama K, Miura K, McErlean CSP, Nomura T. A Stereoselective Strigolactone Biosynthesis Catalyzed by a 2-Oxoglutarate-Dependent Dioxygenase in Sorghum. PLANT & CELL PHYSIOLOGY 2023; 64:1034-1045. [PMID: 37307421 PMCID: PMC10504574 DOI: 10.1093/pcp/pcad060] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/14/2023]
Abstract
Seeds of root parasitic plants, Striga, Orobanche and Phelipanche spp., are induced to germinate by strigolactones (SLs) exudated from host roots. In Striga-resistant cultivars of Sorghum bicolor, the loss-of-function of the Low Germination Stimulant 1 (LGS1) gene changes the major SL from 5-deoxystrigol (5DS) to orobanchol, which has an opposite C-ring stereochemistry. The biosynthetic pathway of 5DS catalyzed by LGS1 has not been fully elucidated. Since other unknown regulators, in addition to LGS1 encoding a sulfotransferase, appear to be necessary for the stereoselective biosynthesis of 5DS, we examined Sobic.005G213500 (Sb3500), encoding a 2-oxoglutarate-dependent dioxygenase, as a candidate regulator, which is co-expressed with LGS1 and located 5'-upstream of LGS1 in the sorghum genome. When LGS1 was expressed with known SL biosynthetic enzyme genes including the cytochrome P450 SbMAX1a in Nicotiana benthamiana leaves, 5DS and its diastereomer 4-deoxyorobanchol (4DO) were produced in approximately equal amounts, while the production of 5DS was significantly larger than that of 4DO when Sb3500 was also co-expressed. We also confirmed the stereoselective 5DS production in an in vitro feeding experiment using synthetic chemicals with recombinant proteins expressed in Escherichia coli and yeast. This finding demonstrates that Sb3500 is a stereoselective regulator in the conversion of the SL precursor carlactone to 5DS, catalyzed by LGS1 and SbMAX1a, providing a detailed understanding of how different SLs are produced to combat parasitic weed infestations.
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Affiliation(s)
- Akiyoshi Yoda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
| | - Kaori Yoneyama
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Research and Development Bureau, Saitama University, Saitama-shi, Saitama, 338-8570 Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan
| | | | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
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11
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Lui ACW, Pow KC, Lin N, Lam LPY, Liu G, Godwin ID, Fan Z, Khoo CJ, Tobimatsu Y, Wang L, Hao Q, Lo C. Regioselective stilbene O-methylations in Saccharinae grasses. Nat Commun 2023; 14:3462. [PMID: 37308495 DOI: 10.1038/s41467-023-38908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 05/18/2023] [Indexed: 06/14/2023] Open
Abstract
O-Methylated stilbenes are prominent nutraceuticals but rarely produced by crops. Here, the inherent ability of two Saccharinae grasses to produce regioselectively O-methylated stilbenes is reported. A stilbene O-methyltransferase, SbSOMT, is first shown to be indispensable for pathogen-inducible pterostilbene (3,5-bis-O-methylated) biosynthesis in sorghum (Sorghum bicolor). Phylogenetic analysis indicates the recruitment of genus-specific SOMTs from canonical caffeic acid O-methyltransferases (COMTs) after the divergence of Sorghum spp. from Saccharum spp. In recombinant enzyme assays, SbSOMT and COMTs regioselectively catalyze O-methylation of stilbene A-ring and B-ring respectively. Subsequently, SOMT-stilbene crystal structures are presented. Whilst SbSOMT shows global structural resemblance to SbCOMT, molecular characterizations illustrate two hydrophobic residues (Ile144/Phe337) crucial for substrate binding orientation leading to 3,5-bis-O-methylations in the A-ring. In contrast, the equivalent residues (Asn128/Asn323) in SbCOMT facilitate an opposite orientation that favors 3'-O-methylation in the B-ring. Consistently, a highly-conserved COMT is likely involved in isorhapontigenin (3'-O-methylated) formation in wounded wild sugarcane (Saccharum spontaneum). Altogether, our work reveals the potential of Saccharinae grasses as a source of O-methylated stilbenes, and rationalize the regioselectivity of SOMT activities for bioengineering of O-methylated stilbenes.
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Affiliation(s)
- Andy C W Lui
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Kah Chee Pow
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Nan Lin
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Lydia Pui Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Tegata Gakuen-machi 1-1, Akita City, Akita, 010-8502, Japan
| | - Guoquan Liu
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhuming Fan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Chen Jing Khoo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Quan Hao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.
- China Spallation Neutron Source, Dongguan, Guangdong, 523000, China.
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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12
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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13
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Zhang B, Lewis JA, Vermerris W, Sattler SE, Kang C. A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids. PLANT PHYSIOLOGY 2023; 192:102-118. [PMID: 36575825 PMCID: PMC10152656 DOI: 10.1093/plphys/kiac604] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 05/03/2023]
Abstract
In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Jacob A Lewis
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, UF Genetics Institute, and Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, Florida 32610, USA
| | - Scott E Sattler
- U.S. Department of Agriculture—Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, Lincoln, Nebraska 68583, USA
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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14
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Shekhar S, Prasad AS, Banjare K, Kaushik A, Mannade AK, Dubey M, Patil A, Premi V, Vishwakarma AK, Sao A, Saxena RR, Dubey A, Chandel G. LMT db: A comprehensive transcriptome database for climate-resilient, nutritionally rich little millet ( Panicum sumatrense). FRONTIERS IN PLANT SCIENCE 2023; 14:1106104. [PMID: 36993866 PMCID: PMC10041709 DOI: 10.3389/fpls.2023.1106104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
Little millet (Panicum sumatrense) a native of Chhattisgarh, belongs to the minor millet group and is primarily known as a climate-resilient and nutritionally rich crop. However, due to the lack of enough Omic studies on the crop, the scientific community has largely remained unaware of the potential of this crop, resulting in less scope for its utilization in crop improvement programs. Looking at global warming, erratic climate change, nutritional security, and limited genetic information available, the Little Millet Transcriptome Database (LMTdb) (https://igkv.ac.in/xenom/index.aspx) was conceptualized upon completion of the transcriptome sequencing of little millet with the aim of deciphering the genetic signatures of this largely unknown crop. The database was developed with the view of providing information about the most comprehensive part of the genome, the 'Transcriptome'. The database includes transcriptome sequence information, functional annotation, microsatellite markers, DEGs, and pathway information. The database is a freely available resource that provides breeders and scientists a portal to search, browse, and query data to facilitate functional and applied Omic studies in millet crops.
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Affiliation(s)
- Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Archana S. Prasad
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Kalpana Banjare
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Abhijeet Kaushik
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Ajit K. Mannade
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Mahima Dubey
- Department of Vegetable Biotechnology, VNR Seeds Private Limited, Raipur, India
| | - Arun Patil
- Department of Vegetable Biotechnology, VNR Seeds Private Limited, Raipur, India
| | - Vinay Premi
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | | | - Abhinav Sao
- Department of Genetics and Plant Breeding, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Ravi R. Saxena
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Amit Dubey
- Chhattisgarh Council of Science and Technology, Raipur, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
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15
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Takanashi H. Genetic control of morphological traits useful for improving sorghum. BREEDING SCIENCE 2023; 73:57-69. [PMID: 37168813 PMCID: PMC10165342 DOI: 10.1270/jsbbs.22069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 05/13/2023]
Abstract
Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C4 crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C4 grasses because of its high morphological diversity and relatively small genome size compared to other C4 grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.
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Affiliation(s)
- Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding author (e-mail: )
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16
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Zhang S, Wang J, He W, Kan S, Liao X, Jordan DR, Mace ES, Tao Y, Cruickshank AW, Klein R, Yuan D, Tembrock LR, Wu Z. Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution. BMC PLANT BIOLOGY 2023; 23:91. [PMID: 36782130 PMCID: PMC9926791 DOI: 10.1186/s12870-023-04104-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism. RESULTS Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa. CONCLUSIONS We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.
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Affiliation(s)
- Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hubei, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Emma S Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, 4370, Australia
| | - Alan W Cruickshank
- Department of Agriculture and Fisheries (DAF), Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland, 4370, Australia
| | - Robert Klein
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, Texas, 77845, USA
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hubei, Wuhan, 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong, Shenzhen, 518120, China.
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17
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Wang L, Zhang J, Wang R, Huang Z, Cui R, Zhu H, Yang Y, Zhang D. Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max). Funct Integr Genomics 2023; 23:37. [PMID: 36639600 DOI: 10.1007/s10142-023-00966-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.
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Affiliation(s)
- Li Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongwen Huang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
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18
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [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: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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19
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Borrell AK, Wong ACS, George-Jaeggli B, van Oosterom EJ, Mace ES, Godwin ID, Liu G, Mullet JE, Klein PE, Hammer GL, McLean G, Hunt C, Jordan DR. Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6711-6726. [PMID: 35961690 PMCID: PMC9629789 DOI: 10.1093/jxb/erac336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/10/2022] [Indexed: 05/27/2023]
Abstract
The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.
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Affiliation(s)
- Andrew K Borrell
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
| | - Albert C S Wong
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Barbara George-Jaeggli
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | | | - Emma S Mace
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - Ian D Godwin
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Guoquan Liu
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Patricia E Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Graeme L Hammer
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Greg McLean
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - David R Jordan
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
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20
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Langella E, Di Fiore A, Alterio V, Monti SM, De Simone G, D’Ambrosio K. α-CAs from Photosynthetic Organisms. Int J Mol Sci 2022; 23:ijms231912045. [PMID: 36233343 PMCID: PMC9570166 DOI: 10.3390/ijms231912045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous enzymes that catalyze the reversible carbon dioxide hydration reaction. Among the eight different CA classes existing in nature, the α-class is the largest one being present in animals, bacteria, protozoa, fungi, and photosynthetic organisms. Although many studies have been reported on these enzymes, few functional, biochemical, and structural data are currently available on α-CAs isolated from photosynthetic organisms. Here, we give an overview of the most recent literature on the topic. In higher plants, these enzymes are engaged in both supplying CO2 at the Rubisco and determining proton concentration in PSII membranes, while in algae and cyanobacteria they are involved in carbon-concentrating mechanism (CCM), photosynthetic reactions and in detecting or signaling changes in the CO2 level in the environment. Crystal structures are only available for three algal α-CAs, thus not allowing to associate specific structural features to cellular localizations or physiological roles. Therefore, further studies on α-CAs from photosynthetic organisms are strongly needed to provide insights into their structure–function relationship.
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21
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Yu KMJ, Oliver J, McKinley B, Weers B, Fabich HT, Evetts N, Conradi MS, Altobelli SA, Marshall-Colon A, Mullet J. Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:476-492. [PMID: 36038985 DOI: 10.1111/tpj.15960] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES (SbLOB), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM (dw2) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non-meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin-dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.
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Affiliation(s)
- Ka Man Jasmine Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Joel Oliver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Hilary T Fabich
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Nathan Evetts
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Mark S Conradi
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Stephen A Altobelli
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois, Champaign-Urbana, Illinois, 61801, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
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22
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Rivai RR, Miyamoto T, Awano T, Yoshinaga A, Chen S, Sugiyama J, Tobimatsu Y, Umezawa T, Kobayashi M. Limiting silicon supply alters lignin content and structures of sorghum seedling cell walls. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111325. [PMID: 35696925 DOI: 10.1016/j.plantsci.2022.111325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sorghum has been recognized as a promising energy crop. The composition and structure of lignin in the cell wall are important factors that affect the quality of plant biomass as a bioenergy feedstock. Silicon (Si) supply may affect the lignin content and structure, as both Si and lignin are possibly involved in plant mechanical strength. However, our understanding regarding the interaction between Si and lignin in sorghum is limited. Therefore, in this study, we analyzed the lignin in the cell walls of sorghum seedlings cultured hydroponically with or without Si supplementation. Limiting the Si supply significantly increased the thioglycolic acid lignin content and thioacidolysis-derived syringyl/guaiacyl monomer ratio. At least part of the modification may be attributable to the change in gene expression, as suggested by the upregulation of phenylpropanoid biosynthesis-related genes under -Si conditions. The cell walls of the -Si plants had a higher mechanical strength and calorific value than those of the +Si plants. These results provide some insights into the enhancement of the value of sorghum biomass as a feedstock for energy production by limiting Si uptake.
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Affiliation(s)
- Reza Ramdan Rivai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan; National Research and Innovation Agency of the Republic of Indonesia, Bogor, Indonesia
| | - Takuji Miyamoto
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Tatsuya Awano
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Arata Yoshinaga
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuoye Chen
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junji Sugiyama
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Masaru Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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23
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Genome-wide identification of chromatin regulators in Sorghum bicolor. 3 Biotech 2022; 12:117. [PMID: 35547013 PMCID: PMC9033926 DOI: 10.1007/s13205-022-03181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/03/2022] [Indexed: 11/01/2022] Open
Abstract
Chromatin regulators play important roles in plant development and stress response. In this study, we identified totally 231 chromatin regulators including 63 histones, 29 histone chaperones, 101 histone modification enzymes, and 38 chromatin remodeling factors from Sorghum bicolor (L.) Moench. Most of these chromatin regulators are homologous to their counterparts in Arabidopsis or rice. However, sorghum genome evolves a few novel histone variants specific to some grass species and a sorghum-unique chromatin remodeling factor that contain the domains belonging to the elongation factor EF-Tu and the histone chaperone SPT16. Finally, we performed co-expression analysis for the chromatin regulator-encoding genes by clustering the expression patterns of these genes. Our results provide useful information for the future studies on the mechanism of epigenetic regulation in sorghum and its roles in development and stress response. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03181-8.
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24
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Zhou Y, Sukul A, Mishler-Elmore JW, Faik A, Held MA. PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum. PLANT & CELL PHYSIOLOGY 2022; 63:565-572. [PMID: 35024864 PMCID: PMC9214644 DOI: 10.1093/pcp/pcac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to civilization. However, co-expression network tools for these plants are lacking. Here, we have constructed global GCNs for barley and sorghum using existing RNA-seq data sets. Meta-information was manually curated and categorized by tissue type to also build tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus. PlantNexus is freely available at https://plantnexus.ohio.edu/.
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Affiliation(s)
- Yadi Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Abhijit Sukul
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | | | - Ahmed Faik
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
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25
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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26
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Fontanet-Manzaneque JB, Blasco-Escámez D, Martignago D, Rico-Medina A, Caño-Delgado AI. A Method for Rapid and Reliable Molecular Detection of Drought-Response Genes in Sorghum bicolor (L.) Moench Roots. Methods Mol Biol 2022; 2539:223-233. [PMID: 35895207 DOI: 10.1007/978-1-0716-2537-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Drought is a major environmental stress that limits growth and productivity in agricultural ecosystems limiting crop yield worldwide. Breeding crops for enhanced drought tolerance is a priority to preserve food security on the increasing world population. Recent work in Arabidopsis has shown that vascular brassinosteroid receptor BRL3 (Brassinosteroid insensitive like-3) transcriptionally controls the production of osmoprotectant metabolites that confer drought resistance without penalizing growth, offering new and exciting possibilities for biotechnological improvement of drought-resistant crops. In cereals, understanding transcriptional responses to drought is an essential step for the production of gene-edited drought-resistant cereals. In this chapter, we present a method to analyze the transcriptional responses to drought in Sorghum bicolor (L.) Moench, our cereal of choice. Among the genes we tested, we found that drought marker gene SbDHN1 has a 1000-fold increase only after 1 day of drought, bringing possibilities for the development of molecular sensors for testing drought. Overall, this analysis is useful to set up conditions of high-throughput transcriptomic analysis of drought stressed plants before drought phenotype is observed.
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Affiliation(s)
- Juan B Fontanet-Manzaneque
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB (CRAG), Barcelona, Spain
| | - David Blasco-Escámez
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB (CRAG), Barcelona, Spain
| | - Damiano Martignago
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB (CRAG), Barcelona, Spain
- Department of Biosciences, University of Milan, Milan, Italy
| | - Andrés Rico-Medina
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB (CRAG), Barcelona, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB (CRAG), Barcelona, Spain.
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27
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Xin Z, Wang M, Cuevas HE, Chen J, Harrison M, Pugh NA, Morris G. Sorghum genetic, genomic, and breeding resources. PLANTA 2021; 254:114. [PMID: 34739592 PMCID: PMC8571242 DOI: 10.1007/s00425-021-03742-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/28/2021] [Indexed: 05/24/2023]
Abstract
Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, and breeding resources that are now available to researchers and plant breeders. As the world faces the challenges of a rising population and a changing global climate, new agricultural solutions will need to be developed to address the food and fiber needs of the future. To that end, sorghum will be an invaluable crop species as it is a stress-resistant C4 plant that is well adapted for semi-arid and arid regions. Sorghum has already remained as a staple food crop in many parts of Africa and Asia and is critically important for animal feed and niche culinary applications in other regions, such as the United States. In addition, sorghum has begun to be developed into a promising feedstock for forage and bioenergy production. Due to this increasing demand for sorghum and its potential to address these needs, the continuous development of powerful community resources is required. These resources include vast collections of sorghum germplasm, high-quality reference genome sequences, sorghum association panels for genome-wide association studies of traits involved in food and bioenergy production, mutant populations for rapid discovery of causative genes for phenotypes relevant to sorghum improvement, gene expression atlas, and online databases that integrate all resources and provide the sorghum community with tools that can be used in breeding and genomic studies. Used in tandem, these valuable resources will ensure that the rate, quality, and collaborative potential of ongoing sorghum improvement efforts is able to rival that of other major crops.
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA.
| | - Mingli Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - Hugo E Cuevas
- Tropical Agriculture Research Station, USDA-ARS, Mayagüez, 00680, Puerto Rico
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Melanie Harrison
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - N Ace Pugh
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Geoffrey Morris
- Crop Quantitative Genomics, Soil and Crop Sciences, Colorado State University, Plant Sciences Building, Fort Collins, CO, 80523, USA
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28
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Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W, Hao H, Jing HC. SorGSD: updating and expanding the sorghum genome science database with new contents and tools. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:165. [PMID: 34344425 PMCID: PMC8336335 DOI: 10.1186/s13068-021-02016-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/24/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits. RESULTS We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/ . CONCLUSIONS SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.
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Affiliation(s)
- Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhonghuang Wang
- University of Chinese Academy of Sciences, Beijing, 100049 China
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Junwei Zhu
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Dongmei Tian
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Cuiping Li
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jingchu Luo
- College of Life Sciences and Center for Bioinformatics, Peking University, Beijing, 100871 China
| | - Wenming Zhao
- University of Chinese Academy of Sciences, Beijing, 100049 China
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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29
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Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review. Life (Basel) 2021; 11:life11070704. [PMID: 34357076 PMCID: PMC8305457 DOI: 10.3390/life11070704] [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: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/29/2022] Open
Abstract
Sorghum is a cereal crop with key agronomic traits of drought and heat stress tolerance, making it an ideal food and industrial commodity for hotter and more arid climates. These stress tolerances also present a useful scientific resource for studying the molecular basis for environmental resilience. Here we provide an extensive review of current transcriptome and proteome works conducted with laboratory, greenhouse, or field-grown sorghum plants exposed to drought, osmotic stress, or treated with the drought stress-regulatory phytohormone, abscisic acid. Large datasets from these studies reveal changes in gene/protein expression across diverse signaling and metabolic pathways. Together, the emerging patterns from these datasets reveal that the overall functional classes of stress-responsive genes/proteins within sorghum are similar to those observed in equivalent studies of other drought-sensitive model species. This highlights a monumental challenge of distinguishing key regulatory genes/proteins, with a primary role in sorghum adaptation to drought, from genes/proteins that change in expression because of stress. Finally, we discuss possible options for taking the research forward. Successful exploitation of sorghum research for implementation in other crops may be critical in establishing climate-resilient agriculture for future food security.
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30
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Breia R, Conde A, Badim H, Fortes AM, Gerós H, Granell A. Plant SWEETs: from sugar transport to plant-pathogen interaction and more unexpected physiological roles. PLANT PHYSIOLOGY 2021; 186:836-852. [PMID: 33724398 PMCID: PMC8195505 DOI: 10.1093/plphys/kiab127] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/05/2021] [Indexed: 05/19/2023]
Abstract
Sugars Will Eventually be Exported Transporters (SWEETs) have important roles in numerous physiological mechanisms where sugar efflux is critical, including phloem loading, nectar secretion, seed nutrient filling, among other less expected functions. They mediate low affinity and high capacity transport, and in angiosperms this family is composed by 20 paralogs on average. As SWEETs facilitate the efflux of sugars, they are highly susceptible to hijacking by pathogens, making them central players in plant-pathogen interaction. For instance, several species from the Xanthomonas genus are able to upregulate the transcription of SWEET transporters in rice (Oryza sativa), upon the secretion of transcription-activator-like effectors. Other pathogens, such as Botrytis cinerea or Erysiphe necator, are also capable of increasing SWEET expression. However, the opposite behavior has been observed in some cases, as overexpression of the tonoplast AtSWEET2 during Pythium irregulare infection restricted sugar availability to the pathogen, rendering plants more resistant. Therefore, a clear-cut role for SWEET transporters during plant-pathogen interactions has so far been difficult to define, as the metabolic signatures and their regulatory nodes, which decide the susceptibility or resistance responses, remain poorly understood. This fuels the still ongoing scientific question: what roles can SWEETs play during plant-pathogen interaction? Likewise, the roles of SWEET transporters in response to abiotic stresses are little understood. Here, in addition to their relevance in biotic stress, we also provide a small glimpse of SWEETs importance during plant abiotic stress, and briefly debate their importance in the particular case of grapevine (Vitis vinifera) due to its socioeconomic impact.
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Affiliation(s)
- Richard Breia
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga 4710-057, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real 5001-801, Portugal
| | - Artur Conde
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga 4710-057, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real 5001-801, Portugal
- Author for communication:
| | - Hélder Badim
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga 4710-057, Portugal
| | - Ana Margarida Fortes
- Lisbon Science Faculty, BioISI, University of Lisbon, Campo Grande, Lisbon 1749-016, Portugal
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga 4710-057, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real 5001-801, Portugal
- Centre of Biological Engineering (CEB), Department of Engineering, University of Minho, Braga 4710-057, Portugal
| | - Antonio Granell
- Institute of Molecular and Cellular Biology of Plants, Spanish National Research Council (CSIC), Polytechnic University of Valencia, Valencia 46022, Spain
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Aono AH, Pimenta RJG, Garcia ALB, Correr FH, Hosaka GK, Carrasco MM, Cardoso-Silva CB, Mancini MC, Sforça DA, dos Santos LB, Nagai JS, Pinto LR, Landell MGDA, Carneiro MS, Balsalobre TW, Quiles MG, Pereira WA, Margarido GRA, de Souza AP. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:668623. [PMID: 34305969 PMCID: PMC8294386 DOI: 10.3389/fpls.2021.668623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.
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Affiliation(s)
- Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo José Gonzaga Pimenta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Guilherme Kenichi Hosaka
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Marishani Marin Carrasco
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Melina Cristina Mancini
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - James Shiniti Nagai
- Faculty of Medicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Thiago Willian Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Marcos Gonçalves Quiles
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (Unifesp), São José dos Campos, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira de Souza,
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32
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Raffan S, Halford NG. Cereal asparagine synthetase genes. THE ANNALS OF APPLIED BIOLOGY 2021; 178:6-22. [PMID: 33518769 PMCID: PMC7818274 DOI: 10.1111/aab.12632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 05/12/2023]
Abstract
Asparagine synthetase catalyses the transfer of an amino group from glutamine to aspartate to form glutamate and asparagine. The accumulation of free (nonprotein) asparagine in crops has implications for food safety because free asparagine is the precursor for acrylamide, a carcinogenic contaminant that forms during high-temperature cooking and processing. Here we review publicly available genome data for asparagine synthetase genes from species of the Pooideae subfamily, including bread wheat and related wheat species (Triticum and Aegilops spp.), barley (Hordeum vulgare) and rye (Secale cereale) of the Triticeae tribe. Also from the Pooideae subfamily: brachypodium (Brachypodium dIstachyon) of the Brachypodiae tribe. More diverse species are also included, comprising sorghum (Sorghum bicolor) and maize (Zea mays) of the Panicoideae subfamily and rice (Oryza sativa) of the Ehrhartoideae subfamily. The asparagine synthetase gene families of the Triticeae species each comprise five genes per genome, with the genes assigned to four groups: 1, 2, 3 (subdivided into 3.1 and 3.2) and 4. Each species has a single gene per genome in each group, except that some bread wheat varieties (genomes AABBDD) and emmer wheat (Triticum dicoccoides; genomes AABB) lack a group 2 gene in the B genome. This raises questions about the ancestry of cultivated pasta wheat and the B genome donor of bread wheat, suggesting that the hybridisation event that gave rise to hexaploid bread wheat occurred more than once. In phylogenetic analyses, genes from the other species cluster with the Triticeae genes, but brachypodium, sorghum and maize lack a group 2 gene, while rice has only two genes, one group 3 and one group 4. This means that TaASN2, the most highly expressed asparagine synthetase gene in wheat grain, has no equivalent in maize, rice, sorghum or brachypodium. An evolutionary pathway is proposed in which a series of gene duplications gave rise to the five genes found in modern Triticeae species.
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Affiliation(s)
- Sarah Raffan
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
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33
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Kumar S, Adiram-Filiba N, Blum S, Sanchez-Lopez JA, Tzfadia O, Omid A, Volpin H, Heifetz Y, Goobes G, Elbaum R. Siliplant1 protein precipitates silica in sorghum silica cells. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6830-6843. [PMID: 32485738 DOI: 10.1093/jxb/eraa258] [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: 01/08/2020] [Accepted: 05/26/2020] [Indexed: 05/26/2023]
Abstract
Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume using an unknown biological factor. Using bioinformatics tools, we identified a previously uncharacterized protein in Sorghum bicolor, which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell types. Our results show that Slp1 precipitates silica in sorghum silica cells.
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Affiliation(s)
- Santosh Kumar
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Shula Blum
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Javier Arturo Sanchez-Lopez
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Oren Tzfadia
- Bioinformatics and Systems Biology, VIB/Ghent University, Gent, Belgium
| | - Ayelet Omid
- Danziger Innovations Limited, Mishmar Hashiva, Israel
| | - Hanne Volpin
- Danziger Innovations Limited, Mishmar Hashiva, Israel
| | - Yael Heifetz
- Department of Entomology, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Rivka Elbaum
- Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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34
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Abdul‐Awal SM, Chen J, Xin Z, Harmon FG. A sorghum gigantea mutant attenuates florigen gene expression and delays flowering time. PLANT DIRECT 2020; 4:e00281. [PMID: 33210074 PMCID: PMC7665845 DOI: 10.1002/pld3.281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
GIGANTEA (GI) is a conserved plant-specific gene that modulates a range of environmental responses in multiple plant species, including playing a key role in photoperiodic regulation of flowering time. The C4 grass Sorghum bicolor is an important grain and subsistence crop, animal forage, and cellulosic biofuel feedstock that is tolerant of abiotic stresses and marginal soils. To understand sorghum flowering time regulatory networks, we characterized the sbgi-ems1 nonsense mutant allele of the sorghum GIGANTEA (SbGI) gene from a sequenced M4 EMS-mutagenized BTx623 population. sbgi-ems1 plants flowered later than wild type siblings under both long-day or short-day photoperiods. Delayed flowering in sbgi-ems1 plants accompanied an increase in node number, indicating an extended vegetative growth phase prior to flowering. sbgi-ems1 plants had reduced expression of floral activator genes SbCO and SbEHD1 and downstream FT-like florigen genes SbFT, SbCN8, and SbCN12. Therefore, SbGI plays a role in regulating SbCO and SbEHD1 expression that serves to accelerate flowering. SbGI protein physically interacts with the sorghum FLAVIN-BINDING, KELCH REPEAT, F-BOX1-like (SbFFL) protein, a conserved flowering-associated blue light photoreceptor, and the SbGI-SbFFL interaction is stimulated by blue light. This work demonstrates that SbGI is an activator of sorghum flowering time upstream of florigen genes under short- and long-day photoperiods, likely in association with the activity of the blue light photoreceptor SbFFL. SIGNIFICANCE STATEMENT This study elucidates molecular details of flowering time networks for the adaptable C4 cereal crop Sorghum bicolor, including demonstration of a role for blue light sensing in sorghum GIGANTEA activity. This work validates the utility of a large publicly available sequenced EMS-mutagenized sorghum population to determine gene function.
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Affiliation(s)
- S. M. Abdul‐Awal
- Plant Gene Expression CenterUSDA‐ARSAlbanyCAUSA
- Department of Plant & Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
- Biotechnology & Genetic Engineering DisciplineKhulna UniversityKhulnaBangladesh
| | - Junping Chen
- Plant Stress and Germplasm Development UnitUSDA‐ARSLubbockTXUSA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development UnitUSDA‐ARSLubbockTXUSA
| | - Frank G. Harmon
- Plant Gene Expression CenterUSDA‐ARSAlbanyCAUSA
- Department of Plant & Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
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35
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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36
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Gaffney J, Tibebu R, Bart R, Beyene G, Girma D, Kane NA, Mace ES, Mockler T, Nickson TE, Taylor N, Zastrow-Hayes G. Open access to genetic sequence data maximizes value to scientists, farmers, and society. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2020. [DOI: 10.1016/j.gfs.2020.100411] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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37
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Wang H, Wang H, Zhang H, Liu S, Wang Y, Gao Y, Xi F, Zhao L, Liu B, Reddy ASN, Lin C, Gu L. The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics 2020; 35:3119-3126. [PMID: 30689723 DOI: 10.1093/bioinformatics/btz038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION MicroRNA (miRNA) and alternative splicing (AS)-mediated post-transcriptional regulation has been extensively studied in most eukaryotes. However, the interplay between AS and miRNAs has not been explored in plants. To our knowledge, the overall profile of miRNA target sites in circular RNAs (circRNA) generated by alternative back splicing has never been reported previously. To address the challenge, we identified miRNA target sites located in alternatively spliced regions of the linear and circular splice isoforms using the up-to-date single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) and Illumina sequencing data in eleven plant species. RESULTS In total, we identified 399 401 and 114 574 AS events from linear and circular RNAs, respectively. Among them, there were 64 781 and 41 146 miRNA target sites located in linear and circular AS region, respectively. In addition, we found 38 913 circRNAs to be overlapping with 45 648 AS events of its own parent isoforms, suggesting circRNA regulation of AS of linear RNAs by forming R-loop with the genomic locus. Here, we present a comprehensive database of miRNA targets in alternatively spliced linear and circRNAs (ASmiR) and a web server for deposition and identification of miRNA target sites located in the alternatively spliced region of linear and circular RNAs. This database is accompanied by an easy-to-use web query interface for meaningful downstream analysis. Plant research community can submit user-defined datasets to the web service to search AS regions harboring small RNA target sites. In conclusion, this study provides an unprecedented resource to understand regulatory relationships between miRNAs and AS in both gymnosperms and angiosperms. AVAILABILITY AND IMPLEMENTATION The readily accessible database and web-based tools are available at http://forestry.fafu.edu.cn/bioinfor/db/ASmiR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology
| | - Sheng Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology.,College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology.,Department of Molecular Cell & Developmental Biology, University of California, Los Angeles, CA, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology
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38
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Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor. G3-GENES GENOMES GENETICS 2020; 10:1511-1520. [PMID: 32132167 PMCID: PMC7202026 DOI: 10.1534/g3.119.400921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.
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39
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Tao Y, Zhao X, Wang X, Hathorn A, Hunt C, Cruickshank AW, van Oosterom EJ, Godwin ID, Mace ES, Jordan DR. Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1093-1105. [PMID: 31659829 PMCID: PMC7061873 DOI: 10.1111/pbi.13284] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/30/2019] [Accepted: 10/24/2019] [Indexed: 05/20/2023]
Abstract
Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Alan W. Cruickshank
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Erik J. van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Ian D. Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Emma S. Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
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40
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Moisseyev G, Park K, Cui A, Freitas D, Rajagopal D, Konda AR, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama EN, Cahoon EB, Zhang C. RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5851117. [PMID: 32500918 PMCID: PMC7273057 DOI: 10.1093/database/baaa038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/02/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Root-associated genes play an important role in plants. Despite the fact that there have been studies on root biology, information on genes that are specifically expressed or upregulated in roots is poorly collected. There exist very few databases dedicated to genes and promoters associated with root biology, preventing effective root-related studies. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and constructed a comprehensive online database of these genes and their promoter sequences. This database creates a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.
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Affiliation(s)
- Gleb Moisseyev
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kiyoul Park
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Cui
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Daniel Freitas
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Divith Rajagopal
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | | | - Mackenzie Mcham
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
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Filiz E, Aydın Akbudak M. Investigation of PIC1 (permease in chloroplasts 1) gene’s role in iron homeostasis: bioinformatics and expression analyses in tomato and sorghum. Biometals 2019; 33:29-44. [DOI: 10.1007/s10534-019-00228-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 11/28/2019] [Indexed: 11/28/2022]
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42
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Lin L, Cai W, Du Z, Zhang W, Xu Q, Sun W, Chen M. Establishing a System for Functional Characterization of Full-Length cDNAs of Camellia sinensis. Int J Mol Sci 2019; 20:ijms20235929. [PMID: 31775391 PMCID: PMC6929147 DOI: 10.3390/ijms20235929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis) is enriched with bioactive secondary metabolites, and is one of the most popular nonalcoholic beverages globally. Two tea reference genomes have been reported; however, the functional analysis of tea genes has lagged, mainly due to tea’s recalcitrance to genetic transformation and the absence of alternative high throughput heterologous expression systems. A full-length cDNA collection with a streamlined cloning system is needed in this economically important woody crop species. RNAs were isolated from nine different vegetative tea tissues, pooled, then used to construct a normalized full-length cDNA library. The titer of unamplified and amplified cDNA library was 6.89 × 106 and 1.8 × 1010 cfu/mL, respectively; the library recombinant rate was 87.2%. Preliminary characterization demonstrated that this collection can complement existing tea reference genomes and facilitate rare gene discovery. In addition, to streamline tea cDNA cloning and functional analysis, a binary vector (pBIG2113SF) was reengineered, seven tea cDNAs isolated from this library were successfully cloned into this vector, then transformed into Arabidopsis. One FL-cDNA, which encodes a putative P1B-type ATPase 5 (CsHMA5), was characterized further as a proof of concept. We demonstrated that overexpression of CsHMA5 in Arabidopsis resulted in copper hyposensitivity. Thus, our data demonstrated that this represents an efficient system for rare gene discovery and functional characterization of tea genes. The integration of a tea FL-cDNA collection with efficient cloning and a heterologous expression system would facilitate functional annotation and characterization of tea genes.
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Affiliation(s)
- Lin Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weiwei Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Zhenghua Du
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Wenjing Zhang
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quanming Xu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
| | - Weijiang Sun
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
| | - Mingjie Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (W.C.); (Z.D.); (Q.X.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-13705067139 (W.S.); +86-18860109236 (M.C.)
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43
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Li Y, Tu M, Feng Y, Wang W, Messing J. Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:274. [PMID: 31832097 PMCID: PMC6868837 DOI: 10.1186/s13068-019-1612-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/09/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Sorghum bicolor (L.) is an important bioenergy source. The stems of sweet sorghum function as carbon sinks and accumulate large amounts of sugars and lignocellulosic biomass and considerable amounts of starch, therefore providing a model of carbon allocation and accumulation for other bioenergy crops. While omics data sets for sugar accumulation have been reported in different genotypes, the common features of primary metabolism in sweet genotypes remain unclear. To obtain a cohesive and comparative picture of carbohydrate metabolism between sorghum genotypes, we compared the phenotypes and transcriptome dynamics of sugar-accumulating internodes among three different sweet genotypes (Della, Rio, and SIL-05) and two non-sweet genotypes (BTx406 and R9188). RESULTS Field experiments showed that Della and Rio had similar dynamics and internode patterns of sugar concentration, albeit distinct other phenotypes. Interestingly, cellulose synthases for primary cell wall and key genes in starch synthesis and degradation were coordinately upregulated in sweet genotypes. Sweet sorghums maintained active monolignol biosynthesis compared to the non-sweet genotypes. Comparative RNA-seq results support the role of candidate Tonoplast Sugar Transporter gene (TST), but not the Sugars Will Eventually be Exported Transporter genes (SWEETs) in the different sugar accumulations between sweet and non-sweet genotypes. CONCLUSIONS Comparisons of the expression dynamics of carbon metabolic genes across the RNA-seq data sets identify several candidate genes with contrasting expression patterns between sweet and non-sweet sorghum lines, including genes required for cellulose and monolignol synthesis (CesA, PTAL, and CCR), starch metabolism (AGPase, SS, SBE, and G6P-translocator SbGPT2), and sucrose metabolism and transport (TPP and TST2). The common transcriptome features of primary metabolism identified here suggest the metabolic networks contributing to carbon sink strength in sorghum internodes, prioritize the candidate genes for manipulating carbon allocation with bioenergy purposes, and provide a comparative and cohesive picture of the complexity of carbon sink strength in sorghum stem.
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Affiliation(s)
- Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Wenqing Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai, 200240 China
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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44
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Diniz AL, Ferreira SS, Ten-Caten F, Margarido GRA, Dos Santos JM, Barbosa GVDS, Carneiro MS, Souza GM. Genomic resources for energy cane breeding in the post genomics era. Comput Struct Biotechnol J 2019; 17:1404-1414. [PMID: 31871586 PMCID: PMC6906722 DOI: 10.1016/j.csbj.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.
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Affiliation(s)
- Augusto L Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Sávio S Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo 05508-090, SP, Brazil
| | - Felipe Ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Gabriel R A Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba 13418-900, SP, Brazil
| | - João M Dos Santos
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Geraldo V de S Barbosa
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Monalisa S Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera km 174, Araras 13600-970, SP, Brazil
| | - Glaucia M Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
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Chen J, Jiao Y, Laza H, Payton P, Ware D, Xin Z. Identification of the First Nuclear Male Sterility Gene (Male-sterile 9) in Sorghum. THE PLANT GENOME 2019; 12:1-12. [PMID: 33016577 DOI: 10.3835/plantgenome2019.03.0020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/03/2019] [Indexed: 06/11/2023]
Abstract
The male-sterile 9 (ms9) is a novel nuclear male-sterile mutant in sorghum. The Ms9 gene encodes a PHD-finger transcription factor critical for pollen development. The identification of the Ms9 gene provides a strategy to control male sterility in sorghum. Nuclear male sterility (NMS) is important for understanding microspore development and could facilitate the development of new strategies to control male sterility. Several NMS lines and mutants have been reported in sorghum [Sorghum bicolor (L.) Moench] previously. However, no male-sterile gene has been identified, hampering the utility of NMS in sorghum breeding. In this study, we characterized a new NMS mutant, male sterile 9 (ms9), which is distinct from all other reported NMS loci. The ms9 mutant is stable under a variety of environmental conditions. Homozygous ms9 plants produced normal ovaries but small pale-colored anthers that contained no pollen grains. Microscopic analyses revealed abnormal microspore development of ms9 at the midmicrospore stage, causing degeneration of microspore inside the anther lobes and male sterility of ms9 plants. Using MutMap, we identified the Ms9 gene as a plant homeotic domain (PHD)-finger transcription factor similar to Ms1 in Arabidopsis thaliana (L.) Heynh. and Ptc1 in rice (Oryza sativa L.). Ms9 is the first NMS gene identified in sorghum. Thus, the Ms9 gene and ms9 mutant provide new genetic tools for studying pollen development and controlling male sterility in sorghum.
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Affiliation(s)
- Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, 79415
| | | | - Haydee Laza
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, 79415
| | - Paxton Payton
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, 79415
| | - Doreen Ware
- Cold Spring Harbor Lab., Cold Spring Harbor, NY
- Soil and Nutrition Lab. Research Unit, USDA-ARS, Cornell Univ., Ithaca, NY
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, 79415
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46
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Gladman N, Jiao Y, Lee YK, Zhang L, Chopra R, Regulski M, Burow G, Hayes C, Christensen SA, Dampanaboina L, Chen J, Burke J, Ware D, Xin Z. Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci 2019; 20:ijms20194951. [PMID: 31597271 PMCID: PMC6801740 DOI: 10.3390/ijms20194951] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
As in other cereal crops, the panicles of sorghum (Sorghum bicolor (L.) Moench) comprise two types of floral spikelets (grass flowers). Only sessile spikelets (SSs) are capable of producing viable grains, whereas pedicellate spikelets (PSs) cease development after initiation and eventually abort. Consequently, grain number per panicle (GNP) is lower than the total number of flowers produced per panicle. The mechanism underlying this differential fertility is not well understood. To investigate this issue, we isolated a series of ethyl methane sulfonate (EMS)-induced multiseeded (msd) mutants that result in full spikelet fertility, effectively doubling GNP. Previously, we showed that MSD1 is a TCP (Teosinte branched/Cycloidea/PCF) transcription factor that regulates jasmonic acid (JA) biosynthesis, and ultimately floral sex organ development. Here, we show that MSD2 encodes a lipoxygenase (LOX) that catalyzes the first committed step of JA biosynthesis. Further, we demonstrate that MSD1 binds to the promoters of MSD2 and other JA pathway genes. Together, these results show that a JA-induced module regulates sorghum panicle development and spikelet fertility. The findings advance our understanding of inflorescence development and could lead to new strategies for increasing GNP and grain yield in sorghum and other cereal crops.
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Affiliation(s)
- Nicholas Gladman
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Yinping Jiao
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Young Koung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- Plasma Technology Research Center, National Fusion Research Institute, 37, Dongjangsan-ro, Gunsan-si, Jeollabuk-do 54004, Korea.
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Ratan Chopra
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Current address: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Shawn A Christensen
- Chemistry Research Unit, USDA-ARS, 1700 S.W. 23RD DRIVE, Gainesville, FL 32608, USA.
| | - Lavanya Dampanaboina
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA.
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
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Lam PY, Lui ACW, Yamamura M, Wang L, Takeda Y, Suzuki S, Liu H, Zhu FY, Chen MX, Zhang J, Umezawa T, Tobimatsu Y, Lo C. Recruitment of specific flavonoid B-ring hydroxylases for two independent biosynthesis pathways of flavone-derived metabolites in grasses. THE NEW PHYTOLOGIST 2019; 223:204-219. [PMID: 30883799 DOI: 10.1111/nph.15795] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/08/2019] [Indexed: 05/19/2023]
Abstract
In rice (Oryza sativa), OsF2H and OsFNSII direct flavanones to independent pathways that form soluble flavone C-glycosides and tricin-type metabolites (both soluble and lignin-bound), respectively. Production of soluble tricin metabolites requires CYP75B4 as a chrysoeriol 5'-hydroxylase. Meanwhile, the close homologue CYP75B3 is a canonical flavonoid 3'-hydroxylase (F3'H). However, their precise roles in the biosynthesis of soluble flavone C-glycosides and tricin-lignins in cell walls remain unknown. We examined CYP75B3 and CYP75B4 expression in vegetative tissues, analyzed extractable flavonoid profiles, cell wall structure and digestibility of their mutants, and investigated catalytic activities of CYP75B4 orthologues in grasses. CYP75B3 and CYP75B4 showed co-expression patterns with OsF2H and OsFNSII, respectively. CYP75B3 is the sole F3'H in flavone C-glycosides biosynthesis, whereas CYP75B4 alone provides sufficient 3',5'-hydroxylation for tricin-lignin deposition. CYP75B4 mutation results in production of apigenin-incorporated lignin and enhancement of cell wall digestibility. Moreover, tricin pathway-specific 3',5'-hydroxylation activities are conserved in sorghum CYP75B97 and switchgrass CYP75B11. CYP75B3 and CYP75B4 represent two different pathway-specific enzymes recruited together with OsF2H and OsFNSII, respectively. Interestingly, the OsF2H-CYP75B3 and OsFNSII-CYP75B4 pairs appear to be conserved in grasses. Finally, manipulation of tricin biosynthesis through CYP75B4 orthologues can be a promising strategy to improve digestibility of grass biomass for biofuel and biomaterial production.
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Affiliation(s)
- Pui Ying Lam
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Andy C W Lui
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Lanxiang Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yuri Takeda
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shiro Suzuki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Hongjia Liu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Mo-Xian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Research Unit for Global Sustainability Studies, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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48
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Jeena GS, Kumar S, Shukla RK. Structure, evolution and diverse physiological roles of SWEET sugar transporters in plants. PLANT MOLECULAR BIOLOGY 2019; 100:351-365. [PMID: 31030374 DOI: 10.1007/s11103-019-00872-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/05/2019] [Indexed: 05/21/2023]
Abstract
Present review describes the structure, evolution, transport mechanism and physiological functions of SWEETs. Their application using TALENs and CRISPR/CAS9 based genomic editing approach is discussed. Sugars Will Eventually be Exported Transporters (SWEET) proteins were first identified in plants as the novel family of sugar transporters which mediates the translocation of sugars across cell membranes. The SWEET family of sugar transporters is unique in terms of their structure which contains seven predicted transmembrane domains with two internal triple-helix bundles which possibly originate due to prokaryotic gene duplication. SWEETs perform diverse physiological functions such as pollen nutrition, nectar secretion, seed filling, phloem loading, and pathogen nutrition which we have discussed in the present review. We also discuss how transcriptional activator-like effector nucleases (TALENs) and CRISPR/CAS9 genome editing tools are used to engineer SWEET mutants which modulate pathogen resistance in plants and its applications in the field of agriculture. The expression of SWEETs promises to implement insights into many other cellular transport mechanisms. To conclude, the present review highlights the recent aspects which will further develop better understanding of molecular evolution, structure, and function of SWEET transporters in plants.
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Affiliation(s)
- Gajendra Singh Jeena
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Sunil Kumar
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
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49
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Ignatova L, Rudenko N, Zhurikova E, Borisova-Mubarakshina M, Ivanov B. Carbonic Anhydrases in Photosynthesizing Cells of C3 Higher Plants. Metabolites 2019; 9:E73. [PMID: 30995746 PMCID: PMC6523093 DOI: 10.3390/metabo9040073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022] Open
Abstract
The review presents data on the location, nature, properties, number, and expression of carbonic anhydrase genes in the photosynthesizing cells of C3 plants. The available data about the presence of carbonic anhydrases in plasma membrane, cytoplasm, mitochondria, chloroplast stroma and thylakoids are scrutinized. Special attention was paid to the presence of carbonic anhydrase activities in the different parts of thylakoids, and on collation of sources of these activities with enzymes encoded by the established genes of carbonic anhydrases. The data are presented to show that the consistent incorporation of carbonic anhydrases belonging to different families of these enzymes forms a coherent system of CO2 molecules transport from air to chloroplasts in photosynthesizing cells, where they are included in organic molecules in the carboxylation reaction. It is discussed that the manifestation of the activity of a certain carbonic anhydrase depends on environmental conditions and the stage of ontogenesis.
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Affiliation(s)
- Lyudmila Ignatova
- Institute of Basic Biological Problems, Federal Research Center ⁻ Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Natalia Rudenko
- Institute of Basic Biological Problems, Federal Research Center ⁻ Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Elena Zhurikova
- Institute of Basic Biological Problems, Federal Research Center ⁻ Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Maria Borisova-Mubarakshina
- Institute of Basic Biological Problems, Federal Research Center ⁻ Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Boris Ivanov
- Institute of Basic Biological Problems, Federal Research Center ⁻ Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia.
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50
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Sanjari S, Shirzadian-Khorramabad R, Shobbar ZS, Shahbazi M. Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum. PLANT CELL REPORTS 2019; 38:361-376. [PMID: 30627770 DOI: 10.1007/s00299-019-02371-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/02/2019] [Indexed: 05/25/2023]
Abstract
SbNAC genes (131) encoding 183 proteins were identified from the sorghum genome and characterized. The expression patterns of SbSNACs were evaluated at three sampling time points under post-flowering drought stress. NAC proteins are specific transcription factors in plants, playing vital roles in development and response to various environmental stresses. Despite the fact that Sorghum bicolor is well-known for its drought-tolerance, it suffers from grain yield loss due to pre and post-flowering drought stress. In the present study, 131 SbNAC genes encoding 183 proteins were identified from the sorghum genome. The phylogenetic trees were constructed based on the NAC domains of sorghum, and also based on sorghum with Arabidopsis and 8 known NAC domains of other plants, which classified the family into 15 and 19 subfamilies, respectively. Based on the obtained results, 13 SbNAC proteins joined the SNAC subfamily, and these proteins are expected to be involved in response to abiotic stresses. Promoter analysis revealed that all SbNAC genes comprise different stress-associated cis-elements in their promoters. UTRs analysis indicated that 101 SbNAC transcripts had upstream open reading frames, while 39 of the transcripts had internal ribosome entry sites in their 5'UTR. Moreover, 298 miRNA target sites were predicted to exist in the UTRs of SbNAC transcripts. The expression patterns of SbSNACs were evaluated in three genotypes at three sampling time points under post-flowering drought stress. Based on the results, it could be suggested that some gene members are involved in response to drought stress at the post-flowering stage since they act as positive or negative transcriptional regulators. Following further functional analyses, some of these genes might be perceived to be promising candidates for breeding programs to enhance drought tolerance in crops.
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Affiliation(s)
- Sepideh Sanjari
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Reza Shirzadian-Khorramabad
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Maryam Shahbazi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran
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