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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Yactayo-Chang JP, Hunter CT, Alborn HT, Christensen SA, Block AK. Production of the Green Leaf Volatile (Z)-3-Hexenal by a Zea mays Hydroperoxide Lyase. PLANTS 2022; 11:plants11172201. [PMID: 36079583 PMCID: PMC9460041 DOI: 10.3390/plants11172201] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
Plant-produced volatile compounds play important roles in plant signaling and in the communication of plants with other organisms. Many plants emit green leaf volatiles (GLVs) in response to damage or attack, which serve to warn neighboring plants or attract predatory or parasitic insects to help defend against insect pests. GLVs include aldehydes, esters, and alcohols of 6-carbon compounds that are released rapidly following wounding. One GLV produced by maize (Zea mays) is the volatile (Z)-3-hexenal; this volatile is produced from the cleavage of (9Z,11E,15Z)-octadecatrienoic acid by hydroperoxide lyases (HPLs) of the cytochrome P450 CYP74B family. The specific HPL in maize involved in (Z)-3-hexenal production had not been determined. In this study, we used phylogenetics with known HPLs from other species to identify a candidate HPL from maize (ZmHPL). To test the ability of the putative HPL to produce (Z)-3-hexenal, we constitutively expressed the gene in Arabidopsis thaliana ecotype Columbia-0 that contains a natural loss-of-function mutant in AtHPL and examined the transgenic plants for restored (Z)-3-hexenal production. Volatile analysis of leaves from these transgenic plants showed that they did produce (Z)-3-hexenal, confirming that ZmHPL can produce (Z)-3-hexenal in vivo. Furthermore, we used gene expression analysis to show that expression of ZmHPL is induced in maize in response to both wounding and the insect pests Spodoptera frugiperda and Spodoptera exigua. Our study demonstrates that ZmHPL can produce GLVs and highlights its likely role in (Z)-3-hexenal production in response to mechanical damage and herbivory in maize.
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Dangol A, Shavit R, Yaakov B, Strickler SR, Jander G, Tzin V. Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids. PLANT MOLECULAR BIOLOGY 2022; 109:533-549. [PMID: 35020104 DOI: 10.1007/s11103-021-01239-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.
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Affiliation(s)
- Anuma Dangol
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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Grover S, Cardona JB, Zogli P, Alvarez S, Naldrett MJ, Sattler SE, Louis J. Reprogramming of sorghum proteome in response to sugarcane aphid infestation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111289. [PMID: 35643611 DOI: 10.1016/j.plantsci.2022.111289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Sugarcane aphid (SCA; Melanaphis sacchari Zehntner) is a key piercing-sucking pest of sorghum (Sorghum bicolor) that cause significant yield losses. While feeding on host plants, complex signaling networks are invoked from recognition of insect attack to induction of plant defenses. Consequently, these signaling networks lead to the production of insecticidal compounds or limited access of nutrients to insects. Previously, several studies were published on the transcriptomics analysis of sorghum in response to SCA infestation, but no information is available on the physiological changes of sorghum at the proteome level. We used the SCA resistant sorghum genotype SC265 for the global proteomics analysis after 1 and 7 days of SCA infestation using the TMT-plex technique. Peptides matching a total of 4211 proteins were identified and 158 proteins were differentially expressed at day 1 and 7. Overall, proteome profiling of SC265 after SCA infestation at days 1 and 7 revealed the suppression of plant defense-related proteins and upregulation of plant defense and signaling-related proteins, respectively. The plant defense responses based on proteome data were validated using electrical penetration graph (EPG) technique to observe changes in aphid feeding. Feeding behavior analyses revealed that SCA spent significantly longer time in phloem phase on SCA infested plants for day 1 and lesser time in day 7 SCA infested sorghum plants, compared to their respective control plants. Overall, our study provides insights into underlying mechanisms that contribute to sorghum resistance to SCA.
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Affiliation(s)
- Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | | | - Prince Zogli
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, US Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583, USA
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln NE 68583, USA.
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Mamidi S, Healey A, Huang P, Grimwood J, Jenkins J, Barry K, Sreedasyam A, Shu S, Lovell JT, Feldman M, Wu J, Yu Y, Chen C, Johnson J, Sakakibara H, Kiba T, Sakurai T, Tavares R, Nusinow DA, Baxter I, Schmutz J, Brutnell TP, Kellogg EA. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol 2020; 38:1203-1210. [PMID: 33020633 PMCID: PMC7536120 DOI: 10.1038/s41587-020-0681-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.
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Affiliation(s)
- Sujan Mamidi
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- BASF Corporation, Durham, NC, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Maximilian Feldman
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, Prosser, WA, USA
| | - Jinxia Wu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Cindy Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
- Multidisciplinary Science Cluster, Kochi University, Nankoku, Kochi, Japan
| | - Rachel Tavares
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas P Brutnell
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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