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Kambara K, Gupta SK, Takano T, Tsugama D. Data from collection and analysis of RNA sequencing data from pearl millet. Data Brief 2024; 55:110592. [PMID: 38993231 PMCID: PMC11237866 DOI: 10.1016/j.dib.2024.110592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Pearl millet (Pennisetum glaucum, also known as Cenchrus americanus) is a cereal crop that has a C4 photosynthesis system and that can grow and develop seeds even under stressed conditions including drought-stressed, high temperature-stressed and nutrient-poor conditions. In previous studies, transcriptomes of pearl millet were studied by RNA sequencing (RNA-Seq) to understand mechanisms regulating its development and tolerance to such stressed conditions. Here, RNA-Seq reads from 565 pearl millet samples from 25 projects in the NCBI (National Center for Biotechnology Information) BioProject database were collected and mapped to the pearl millet reference genome to obtain read counts and transcripts per million (TPM) for each pearl millet gene. The count and TPM data for all the 565 samples as well as the attributes of those samples and projects were deposited in the figshare repository (https://doi.org/10.6084/m9.figshare.24902100).
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Affiliation(s)
- Kota Kambara
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
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Pahari S, Vaid N, Soolanayakanahally R, Kagale S, Pasha A, Esteban E, Provart N, Stobbs JA, Vu M, Meira D, Karunakaran C, Boda P, Prasannakumar MK, Nagaraja A, Jain AK. Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:577-594. [PMID: 38576267 DOI: 10.1111/tpj.16749] [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: 09/02/2022] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.
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Affiliation(s)
- Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Miranda Vu
- Canadian Light Source Inc, Saskatoon, Saskatchewan, Canada
| | - Debora Meira
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, United States
| | | | - Praveen Boda
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | | | - Alur Nagaraja
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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Daduwal HS, Bhardwaj R, Srivastava RK. Pearl millet a promising fodder crop for changing climate: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:169. [PMID: 38913173 DOI: 10.1007/s00122-024-04671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The agricultural sector faces colossal challenges amid environmental changes and a burgeoning human population. In this context, crops must adapt to evolving climatic conditions while meeting increasing production demands. The dairy industry is anticipated to hold the highest value in the agriculture sector in future. The rise in the livestock population is expected to result in an increased demand for fodder feed. Consequently, it is crucial to seek alternative options, as crops demand fewer resources and are resilient to climate change. Pearl millet offers an apposite key to these bottlenecks, as it is a promising climate resilience crop with significantly low energy, water and carbon footprints compared to other crops. Numerous studies have explored its potential as a fodder crop, revealing promising performance. Despite its capabilities, pearl millet has often been overlooked. To date, few efforts have been made to document molecular aspects of fodder-related traits. However, several QTLs and candidate genes related to forage quality have been identified in other fodder crops, which can be harnessed to enhance the forage quality of pearl millet. Lately, excellent genomic resources have been developed in pearl millet allowing deployment of cutting-edge genomics-assisted breeding for achieving a higher rate of genetic gains. This review would facilitate a deeper understanding of various aspects of fodder pearl millet in retrospect along with the future challenges and their solution. This knowledge may pave the way for designing efficient breeding strategies in pearl millet thereby supporting sustainable agriculture and livestock production in a changing world.
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Affiliation(s)
- Harmanpreet Singh Daduwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Ruchika Bhardwaj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India.
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Moin M, Bommineni PR, Tyagi W. Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits. BMC Genomics 2024; 25:581. [PMID: 38858648 PMCID: PMC11165789 DOI: 10.1186/s12864-024-10504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. RESULTS In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. CONCLUSIONS The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.
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Affiliation(s)
- Mazahar Moin
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Pradeep Reddy Bommineni
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Wang S, Xing W, Li W, Xie Z, Xiao Y, Huang W. Red light mitigates Cd toxicity in Egeria densa by restricting Cd accumulation and modulating antioxidant defense system. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108675. [PMID: 38705047 DOI: 10.1016/j.plaphy.2024.108675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/21/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Controlling light qualities have been acknowledged as an effective method to enhance the efficiency of phytoremediation, as light has a significant impact on plant growth. This study examined the effects of light qualities on cadmium (Cd) tolerance in aquatic plant Egeria densa using a combination of biochemical and transcriptomic approaches. The study revealed that E. densa exhibits higher resistance to Cd toxicity under red light (R) compared to blue light (B), as evidenced by a significant decrease in photosynthetic inhibition and damage to organelle ultrastructure. After Cd exposure, there was a significantly reduced Cd accumulation and enhanced levels of both glutathione reductase (GR) activity and glutathione (GSH), along with an increase in jasmonic acid (JA) in R-grown E. densa compared to B. Transcriptional analysis revealed that R caused an up-regulation of Cd transporter genes such as ABCG (G-type ATP-binding cassette transporter), ABCC (C-type ATP-binding cassette transporter), and CAX2 (Cation/H+ exchanger 2), while down-regulated the expression of HIPP26 (Heavy metal-associated isoprenylated plant protein 26), resulting in reduced Cd uptake and enhanced Cd exportation and sequestration into vacuoles. Moreover, the expression of genes involved in phytochromes and JA synthesis was up-regulated in Cd treated E. densa under R. In summary, the results suggest that R could limit Cd accumulation and improve antioxidant defense to mitigate Cd toxicity in E. densa, which might be attributed to the enhanced JA and phytochromes. This study provides a foundation for using light control methods with aquatic macrophytes to remediate heavy metal contamination in aquatic systems.
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Affiliation(s)
- Shanwei Wang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Wei Xing
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wei Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Yani Wetland Ecosystem Positioning Observation and Research Station, Tibet University, Lhasa, China; Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, Tibet University, Lhasa, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zuoming Xie
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Yuan Xiao
- The Analysis and Testing Center of Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenmin Huang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Bhavani P, Nandini C, Maharajan T, Ningaraju TM, Nandini B, Parveen SG, Pushpa K, Ravikumar RL, Nagaraja TE, Ceasar SA. Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement. PLANTA 2024; 260:10. [PMID: 38796805 DOI: 10.1007/s00425-024-04446-7] [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: 02/15/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
MAIN CONCLUSION Brown-top millet is a lesser-known millet with a high grain nutrient value, early maturation, and drought tolerance that needs basic research to understand and conserve food security. Brown-top millet [Urochloa ramosa (L.)] is currently cultivated in some developing countries (especially in India) for food and fodder, although it is less known among the small millets. Like other millets, it contains macro- and micronutrients, vitamins, minerals, proteins, and fiber, all of which have rich health benefits. The nutritional importance and health benefits of brown-top millet are still unknown to many people due to a lack of awareness, wide cultivation, and research. Hence, this millet is currently overshadowed by other major cereals. This review article aims to present the nutritional, breeding, genetic, and genomic resources of brown-top millet to inform millet and other plant researchers. It is important to note that genetic and genomic resources have not yet been created for this millet. To date, there are no genomic and transcriptomic resources for brown-top millet to develop single nucleotide polymorphisms (SNP) and insertion/Deletions (InDels) for breeding studies. Furthermore, studies regarding nutritional significance and health benefits are required to investigate the exact nutritional contents and health benefits of the brown-top millet. The present review delves into the nutritional value and health advantages of brown-top millet, as supported by the available literature. The limitations of producing brown-top millet have been enumerated. We also cover the status of marker-assisted breeding and functional genomics research on closely related species. Lastly, we draw insights for further research such as developing omics resources and applying genome editing to study and improve brown-top millet. This review will help to start breeding and other molecular studies to increase the growth and development of this cereal.
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Affiliation(s)
- P Bhavani
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India.
| | - C Nandini
- Zonal Agricultural and Horticultural Research Station, Babbur Farm, Hiriyur, KSNUAHS, Shivamogga, Karnataka, India.
| | - Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
| | - T M Ningaraju
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - B Nandini
- College of Horticulture, Kolar, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - S Gazala Parveen
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - K Pushpa
- Department of Agronomy, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - R L Ravikumar
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - T E Nagaraja
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [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: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Schillaci M, Zampieri E, Brunetti C, Gori A, Sillo F. Root transcriptomic provides insights on molecular mechanisms involved in the tolerance to water deficit in Pisum sativum inoculated with Pseudomonas sp. PLANTA 2023; 259:33. [PMID: 38160210 DOI: 10.1007/s00425-023-04310-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
MAIN CONCLUSION Root transcriptomics and biochemical analyses in water-stressed Pisum sativum plants inoculated with Pseudomonas spp. suggested preservation of ABA-related pathway and ROS detoxification, resulting in an improved tolerance to stress. Drought already affects agriculture in large areas of the globe and, due to climate change, these areas are predicted to become increasingly unsuitable for agriculture. For several years, plant growth-promoting bacteria (PGPB) have been used to improve legume yields, but many aspects of this interaction are still unclear. To elucidate the mechanisms through which root-associated PGPB can promote plant growth in dry environments, we investigated the response of pea plants inoculated with a potentially beneficial Pseudomonas strain (PK6) and subjected to two different water regimes. Combined biometric, biochemical, and root RNA-seq analyses revealed that PK6 improved pea growth specifically under water deficit, as inoculated plants showed an increased biomass, larger leaves, and longer roots. Abscisic acid (ABA) and proline quantification, together with the transcriptome analysis, suggested that PK6-inoculated plant response to water deficit was more diversified compared to non-inoculated plants, involving alternative metabolic pathways for the detoxification of reactive oxygen species (ROS) and the preservation of the ABA stress signaling pathway. We suggest that the metabolic response of PK6-inoculated plants was more effective in their adaptation to water deprivation, leading to their improved biometric traits. Besides confirming the positive role that PGPB can have in the growth of a legume crop under adverse conditions, this study offers novel information on the mechanisms regulating plant-bacteria interaction under varying water availability. These mechanisms and the involved genes could be exploited in the future for the development of legume varieties, which can profitably grow in dry climates.
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Affiliation(s)
- Martino Schillaci
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy
| | - Elisa Zampieri
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy
| | - Cecilia Brunetti
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, Italy
| | - Antonella Gori
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Fabiano Sillo
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy.
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Nawaz M, Sun J, Shabbir S, Khattak WA, Ren G, Nie X, Bo Y, Javed Q, Du D, Sonne C. A review of plants strategies to resist biotic and abiotic environmental stressors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165832. [PMID: 37524179 DOI: 10.1016/j.scitotenv.2023.165832] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Plants exposed to a variety of abiotic and biotic stressors including environmental pollution and global warming pose significant threats to biodiversity and ecosystem services. Despite substantial literature documenting how plants adapt to distinct stressors, there still is a lack of knowledge regarding responses to multiple stressors and how these affects growth and development. Exposure of plants to concurrent biotic and abiotic stressors such as cadmium and drought, leads to pronounced inhibition in above ground biomass, imbalance in oxidative homeostasis, nutrient assimilation and stunted root growth, elucidating the synergistic interactions of multiple stressors culminating in adverse physiological outcomes. Impact of elevated heavy metal and water deficit exposure extends beyond growth and development, influencing the biodiversity of the microenvironment including the rhizosphere nutrient profile and microbiome. These findings have significant implications for plant-stress interactions and ecosystem functioning that prompt immediate action in order to eliminate effect of pollution and address global environmental issues to promote sustainable tolerance for multiple stress combinations in plants. Here, we review plant tolerance against stress combinations, highlighting the need for interdisciplinary approaches and advanced technologies, such as omics and molecular tools, to achieve a comprehensive understanding of underlying stress tolerance mechanisms. To accelerate progress towards developing stress-tolerance in plants against multiple environmental stressors, future research in plant stress tolerance should adopt a collaborative approach, involving researchers from multiple disciplines with diverse expertise and resources.
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Affiliation(s)
- Mohsin Nawaz
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianfan Sun
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Samina Shabbir
- Department of Chemistry, The Women University Multan, Pakistan
| | - Wajid Ali Khattak
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Guangqian Ren
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yanwen Bo
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Qaiser Javed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Christian Sonne
- Aarhus University, Faculty of Technological Sciences, Department of Ecoscience, Frederiksborgvej 399, 358, DK-4000 Roskilde, Denmark; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
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10
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Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. PLANT METHODS 2023; 19:112. [PMID: 37865785 PMCID: PMC10589961 DOI: 10.1186/s13007-023-01091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript libraries. However, the value of including libraries of differing sizes has not been established. METHODS A comprehensive transcriptome of the leaves of Jojoba (Simmondsia chinensis) was generated from two different PacBio library preparations: standard workflow (SW) and long workflow (LW). RESULTS The importance of using both transcript groups in the analysis was demonstrated by the high proportion of unique sequences (74.6%) that were not shared between the groups. A total of 37.8% longer transcripts were only detected in the long dataset. The completeness of the combined transcriptome was indicated by the presence of 98.7% of genes predicted in the jojoba male reference genome. The high coverage of the transcriptome was further confirmed by BUSCO analysis showing the presence of 96.9% of the genes from the core viridiplantae_odb10 lineage. The high-quality isoforms post Cd-Hit merged dataset of the two workflows had a total of 167,866 isoforms. Most of the transcript isoforms were protein-coding sequences (71.7%) containing open reading frames (ORFs) ≥ 100 amino acids (aa). Alternative splicing and intron retention were the basis of most transcript diversity when analysed at the whole genome level and by specific analysis of the apetala2 gene families. CONCLUSION This suggests the need to specifically target the capture of longer transcripts to provide more comprehensive genome coverage in plant transcriptome analysis and reveal the high level of alternative splicing.
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Affiliation(s)
- Othman Al-Dossary
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Ardashir KharabianMasouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Ibrahim Al-Mssallem
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
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Narayanrao DR, Tomar RS, Sm P, Jasminkumar K, Ashish G, Chauhan NM, Singh SC, Upadhye V, Kuddus M, Kamble L, Hajare ST. De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.). Funct Integr Genomics 2023; 23:303. [PMID: 37723408 DOI: 10.1007/s10142-023-01221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
The genome size of the little millet Panicum sumatrense is unknown, although its genome is fairly diploid (2n = 4x = 36). Despite tremendous nutritional value and adaptability to adverse climatic conditions, P. sumatrense use was limited by their low palatability, coarse grain, and lack of variety of culinary preparations. Hence, understanding how to vary their usage to offer food and nutritional security in the continuously changing modern world, the proposed study was aimed to determine potential genes and metabolites implicated in drought resistance. The drought-resistant genotype of tiny millet OLM-203/Tarini was offered in pots under both relaxed and demanding circumstances. The experimental seedlings were 32 days old and had been under water stress for 23 days. A total of 7606 genes were compared between 23 and 32 days for roots and 7264 total genes were compared between 23 and 32 days for leaves, according to a research on differential expression genes (DEGs). Twenty essential genes for drought tolerance were up-or down-regulated in the control and treated roots of the OLM-203 genotype. For instance, the genes RS193 and XB34 were up-regulated in leaves while, WLIM1 was found to be down-regulated. Gene SKI35 was up-regulated in roots, whereas MPK6 and TCMOp1 were down-regulated in root samples. The roots and leaves of the tiny millet OLM-203 genotype expressed 36 up-regulated and 21 down-regulated serine transcripts, respectively. Gene annotations for leaf samples were classified as having "molecular function" (46%), "cellular component" (19%), and "biological process" (35%), while root sample gene annotations were categorized as having "biological process" (573 contigs), "molecular function" (401 contigs), and "cellular components" (166 contigs). Noteworthy, polyamines play a crucial role in drought stress tolerance in the genotype, and it was found that top ten DEGs encoding for polyamines were common in two tissues (leaf and root). Collectively, transcriptomics profiling (RNA-seq) unveiled transcriptional stability drought stress provide a new insight in underlying modus of operandi in little millet genotype "OLM-203/Tarini" in response to heat stress.
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Affiliation(s)
| | - R S Tomar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Padhiyar Sm
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Kheni Jasminkumar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Gulwe Ashish
- Department of Bioinformatics, Sub Campus Latur, Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Nitin Mahendra Chauhan
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia
| | | | - Vijay Upadhye
- Research and Development Cell (RDC), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Laxmikant Kamble
- Deputy Director and Associate Professor (CD4D), Parul University, Vadodara, Gujarat, India
- Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Sunil Tulshiram Hajare
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia.
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12
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [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: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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13
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Shinde H, Dudhate A, Sathe A, Paserkar N, Wagh SG, Kadam US. Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet. PLANTS (BASEL, SWITZERLAND) 2023; 12:1412. [PMID: 36987099 PMCID: PMC10057621 DOI: 10.3390/plants12061412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress by using "weighted gene coexpression network analysis" (WGCNA) and clustering changes in physiological traits, i.e., CC and RWC associated with gene expression. Genes' correlations with traits were defined in the form of modules, and different color names were used to denote a particular module. Modules are groups of genes with similar patterns of expression, which also tend to be functionally related and co-regulated. In WGCNA, the dark green module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the dark green module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Furthermore, the pathway analysis of these clusters identified the ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet.
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Affiliation(s)
- Harshraj Shinde
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA
| | - Ambika Dudhate
- Sequencing and Discovery Genomics Center, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Atul Sathe
- Plant Science Department, McGill University, Macdonald Campus, Sainte Anne de Bellevue, QC H9X 3V9, Canada
| | - Neha Paserkar
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sopan Ganpatrao Wagh
- Department of Adaptive Biotechnology, Global Change Research Institute of the Czech Academy of Sciences, 60300 Brno, Czech Republic
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science (BK21 Four), Gyeongsang National University, Jinju-Daero, Jinju 52828, Gyeongnam-do, Republic of Korea
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14
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Kumar A, Sheoran P, Mann A, Yadav D, Kumar A, Devi S, Kumar N, Dhansu P, Sharma DK. Deciphering trait associated morpho-physiological responses in pearlmillet hybrids and inbred lines under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1121805. [PMID: 36938010 PMCID: PMC10018183 DOI: 10.3389/fpls.2023.1121805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Pearl millet is a staple food for more than 90 million people residing in highly vulnerable hot arid and semi-arid regions of Africa and Asia. These regions are more prone to detrimental effects of soil salinity on crop performance in terms of reduced biomass and crop yields. We investigated the physiological mechanisms of salt tolerance to irrigation induced salinity stress (ECiw ~3, 6 & 9 dSm-1) and their confounding effects on plant growth and yield in pearl millet inbred lines and hybrids. On average, nearly 30% reduction in above ground plant biomass was observed at ECiw ~6 dSm-1 which stretched to 56% at ECiw ~9 dSm-1 in comparison to best available water. With increasing salinity stress, the crop performance of test hybrids was better in comparison to inbred lines; exhibiting relatively higher stomatal conductance (gS; 16%), accumulated lower proline (Pro; -12%) and shoot Na+/K+(-31%), synthesized more protein (SP; 2%) and sugars (TSS; 32%) compensating in lower biomass (AGB; -22%) and grain yield (GY: -14%) reductions at highest salinity stress of ECiw ~9 dSm-1. Physiological traits modeling underpinning plant salt tolerance and adaptation mechanism illustrated the key role of 7 traits (AGB, Pro, SS, gS, SPAD, Pn, and SP) in hybrids and 8 traits (AGB, Pro, PH, Na+, K+, Na+/K+, SPAD, and gS) in inbred lines towards anticipated grain yield variations in salinity stressed pearl millet. Most importantly, the AGB alone, explained >91% of yield variation among evaluated hybrids and inbreed lines at ECiw ~9 dSm-1. Cumulatively, the better morpho-physiological adaptation and lesser yield reduction with increasing salinity stress in pearl millet hybrids (HHB 146, HHB 272, and HHB 234) and inbred lines (H77/833-2-202, ICMA 94555 and ICMA 843-22) substantially complemented in increased plant salt tolerance and yield stability over a broad range of salinity stress. The information generated herein will help address in deciphering the trait associated physiological alterations to irrigation induced salt stress, and developing potential hybrids in pearl millet using these parents with special characteristics.
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Affiliation(s)
- Ashwani Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Parvender Sheoran
- Division of Social Sciences Research, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Anita Mann
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Devvart Yadav
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Arvind Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Sunita Devi
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Naresh Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
- Department of Chemistry and Biochemistry Eternal University, Baru, Sahib, India
| | - Pooja Dhansu
- ICAR–Sugarcane Breeding Institute, Regional Center, Karnal, India
| | - Dinesh K. Sharma
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
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15
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Shrestha N, Hu H, Shrestha K, Doust AN. Pearl millet response to drought: A review. FRONTIERS IN PLANT SCIENCE 2023; 14:1059574. [PMID: 36844091 PMCID: PMC9955113 DOI: 10.3389/fpls.2023.1059574] [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: 10/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The C4 grass pearl millet is one of the most drought tolerant cereals and is primarily grown in marginal areas where annual rainfall is low and intermittent. It was domesticated in sub-Saharan Africa, and several studies have found that it uses a combination of morphological and physiological traits to successfully resist drought. This review explores the short term and long-term responses of pearl millet that enables it to either tolerate, avoid, escape, or recover from drought stress. The response to short term drought reveals fine tuning of osmotic adjustment, stomatal conductance, and ROS scavenging ability, along with ABA and ethylene transduction. Equally important are longer term developmental plasticity in tillering, root development, leaf adaptations and flowering time that can both help avoid the worst water stress and recover some of the yield losses via asynchronous tiller production. We examine genes related to drought resistance that were identified through individual transcriptomic studies and through our combined analysis of previous studies. From the combined analysis, we found 94 genes that were differentially expressed in both vegetative and reproductive stages under drought stress. Among them is a tight cluster of genes that are directly related to biotic and abiotic stress, as well as carbon metabolism, and hormonal pathways. We suggest that knowledge of gene expression patterns in tiller buds, inflorescences and rooting tips will be important for understanding the growth responses of pearl millet and the trade-offs at play in the response of this crop to drought. Much remains to be learnt about how pearl millet's unique combination of genetic and physiological mechanisms allow it to achieve such high drought tolerance, and the answers to be found may well be useful for crops other than just pearl millet.
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Affiliation(s)
- Nikee Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hao Hu
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
| | - Kumar Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
| | - Andrew N. Doust
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
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16
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Subramani M, Urrea CA, Habib R, Bhide K, Thimmapuram J, Kalavacharla V. Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean ( Phaseolus vulgaris L.) in Response to Terminal Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010210. [PMID: 36616341 PMCID: PMC9824821 DOI: 10.3390/plants12010210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 06/10/2023]
Abstract
We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Carlos A. Urrea
- Panhandle Research and Extension Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA
| | - Rasheed Habib
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Ketaki Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907, USA
| | | | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
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17
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Muhammad HK, Muhammad HL, Njobeh PB, Monjerezi M, Matumba L, Makun HA. Mycotoxin levels and characterization of natural anti-fungal phytochemicals in pearl millet (Pennisetum glaucum) from Nigeria's six agroecological zones. Mycotoxin Res 2022; 38:243-252. [PMID: 35922686 DOI: 10.1007/s12550-022-00465-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
This study reports levels of multiple mycotoxins across Nigeria's six agro-ecological zones and corresponding levels of natural anti-fungal phytochemicals present in pearl millet (PM). 220 representative composite samples of PM were collected for mycotoxin analysis using ultrahigh performance liquid chromatography-mass spectrometry (UHPLC-MS), and 24 were randomly selected for determination of metabolites using gas chromatography-high resolution time of flight-mass spectrometry (GC-HRTOF-MS). In total, 15 mycotoxins were detected, all with levels below the European Union (EU) permissible limits and level of aflatoxins only up to 1.34 µg/kg. This is in sharp contrast to high levels of mycotoxins reported in maize samples from the same agroecological zones. Phytochemical analysis of the same samples identified a total of 88 metabolites, 30 of which are known anti-fungal properties from other previously published studies. The most common of these include methyl ester, bis (2-ethylhexyl) phthalate, and ç-tocopherol. The number of anti-fungal metabolites recovered from each sample ranged from 3 to 17 and varied widely in both number and composition across the agroecological zones. The anti-fungal metabolites may probably make PM less susceptible to fungal proliferation compared to other grains. Hence, it is worth exploring for possible sources of biological control products from PM.
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Affiliation(s)
- Hadiza Kudu Muhammad
- Food and Toxicology Research Group (FTRG), Department of Biochemistry, Federal University of Technology, P.M.B. 65, Minna, Nigeria.
- Department of Biotechnology and Food Technology, Doornfontein Campus, University of Johannesburg, P.O. Box 17011, Gauteng, 2028, South Africa.
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology Minna, Minna, Nigeria.
| | - Hadiza Lami Muhammad
- Food and Toxicology Research Group (FTRG), Department of Biochemistry, Federal University of Technology, P.M.B. 65, Minna, Nigeria
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology Minna, Minna, Nigeria
| | - Patrick Berka Njobeh
- Department of Biotechnology and Food Technology, Doornfontein Campus, University of Johannesburg, P.O. Box 17011, Gauteng, 2028, South Africa
| | - Maurice Monjerezi
- Department of Chemistry, University of Malawi, P.O. Box 280, Zomba, Malawi
| | - Limbikani Matumba
- Food Technology and Nutrition Group-NRC, Lilongwe University of Agriculture and Natural Resources (LUANAR), P.O. Box 143, Lilongwe, Malawi
| | - Hussaini Anthony Makun
- Food and Toxicology Research Group (FTRG), Department of Biochemistry, Federal University of Technology, P.M.B. 65, Minna, Nigeria
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology Minna, Minna, Nigeria
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Han F, Sun M, He W, Guo S, Feng J, Wang H, Yang Q, Pan H, Lou Y, Zhuge Y. Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet ( Setaria italica L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:1864. [PMID: 35890498 PMCID: PMC9323065 DOI: 10.3390/plants11141864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.
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Affiliation(s)
- Fei Han
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Mingjie Sun
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Wei He
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Shuqing Guo
- College of Agronomy, Northwest A&F University, Xianyang 712100, China;
| | - Jingyi Feng
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Hui Wang
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Quangang Yang
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Hong Pan
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Yanhong Lou
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
| | - Yuping Zhuge
- National Engineering Research Center for the Efficient Utilization of Soil and Fertilizer, College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China; (F.H.); (M.S.); (W.H.); (J.F.); (H.W.); (Q.Y.); (H.P.)
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19
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Singh M, Nara U. Genetic insights in pearl millet breeding in the genomic era: challenges and prospects. PLANT BIOTECHNOLOGY REPORTS 2022; 17:15-37. [PMID: 35692233 PMCID: PMC9169599 DOI: 10.1007/s11816-022-00767-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 05/28/2023]
Abstract
Pearl millet, a vital staple food and an important cereal, is emerging as crop having various end-uses as feed, food as well as fodder. Advancement in high-throughput sequencing technology has boosted up pearl millet genomic research in past few years. The available draft genome of pearl millet providing an insight into the advancement of several breeding lines. Comparative and functional genomics have untangled several loci and genes regulating adaptive and agronomic traits in pearl millet. Additionally, the knowledge achieved has far away from being applicable in real breeding practices. We believe that the best path ahead is to adopt genome-based approaches for tailored designing of pearl millet as multi-functional crop with outstanding agronomic traits for various end uses. Presently review highlight several novel concepts and techniques in crop breeding, and summarize the recent advances in pearl millet genomic research, peculiarly genome-wide association dissections of several novel alleles and genes for agronomically important traits.
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Affiliation(s)
- Mandeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Usha Nara
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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20
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Maibam A, Lone SA, Ningombam S, Gaikwad K, Amitha Mithra SV, Singh MP, Singh SP, Dalal M, Padaria JC. Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses. Front Genet 2022; 13:884106. [PMID: 35719375 PMCID: PMC9201763 DOI: 10.3389/fgene.2022.884106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pennisetum glaucum (L.) R. Br., being widely grown in dry and hot weather, frequently encounters heat stress at various stages of growth. The crop, due to its inherent capacity, efficiently overcomes such stress during vegetative stages. However, the same is not always the case with the terminal (flowering through grain filling) stages of growth, where recovery from stress is more challenging. However, certain pearl millet genotypes such as 841-B are known to overcome heat stress even at the terminal growth stages. Therefore, we performed RNA sequencing of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42°C for 6 h) at flowering stages. Over 274 million high quality reads with an average length of 150 nt were generated, which were assembled into 47,310 unigenes having an average length of 1,254 nucleotides, N50 length of 1853 nucleotides, and GC content of 53.11%. Blastx resulted in the annotation of 35,628 unigenes, and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms. A total of 13,786 unigenes were allocated to 23 Clusters of Orthologous Groups, and 4,255 unigenes were distributed to 132 functional Kyoto Encyclopedia of Genes and Genomes database pathways. A total of 12,976 simple sequence repeats and 305,759 SNPs were identified in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidate genes were selected based on log2 fold change and adjusted p value parameters for their differential gene expression by qRT-PCR. We were able to identify differentially expressed genes unique to either of the two genotypes, and also, some DEGs common to both the genotypes were enriched. The differential expression patterns suggested that 841-B 6 h has better ability to maintain homeostasis during heat stress as compared to PPMI-69 6 h. The sequencing data generated in this study, like the SSRs and SNPs, shall serve as an important resource for the development of genetic markers, and the differentially expressed heat responsive genes shall be used for the development of transgenic crops.
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Affiliation(s)
- Albert Maibam
- PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Showkat Ahmad Lone
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Sunil Ningombam
- PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - S. V. Amitha Mithra
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research -Indian Agricultural Research Institute, New Delhi, India
| | - Sumer Pal Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Monika Dalal
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Jasdeep Chatrath Padaria
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
- *Correspondence: Jasdeep Chatrath Padaria,
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Suresh BV, Choudhary P, Aggarwal PR, Rana S, Singh RK, Ravikesavan R, Prasad M, Muthamilarasan M. De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.). Genomics 2022; 114:110347. [PMID: 35337948 DOI: 10.1016/j.ygeno.2022.110347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 01/14/2023]
Abstract
Kodo millet (Paspalum scrobiculatum L.) is a small millet species known for its excellent nutritional and climate-resilient traits. To understand the genes and pathways underlying dehydration stress tolerance of kodo millet, the transcriptome of cultivar 'CO3' subjected to dehydration stress (0 h, 3 h, and 6 h) was sequenced. The study generated 239.1 million clean reads that identified 9201, 9814, and 2346 differentially expressed genes (DEGs) in 0 h vs. 3 h, 0 h vs. 6 h, and 3 h vs. 6 h libraries, respectively. The DEGs were found to be associated with vital molecular pathways, including hormone metabolism and signaling, antioxidant scavenging, photosynthesis, and cellular metabolism, and were validated using qRT-PCR. Also, a higher abundance of uncharacterized genes expressed during stress warrants further studies to characterize this class of genes to understand their role in dehydration stress response. Altogether, the study provides insights into the transcriptomic response of kodo millet during dehydration stress.
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Affiliation(s)
- Bonthala Venkata Suresh
- Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf 40225, Germany.
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
| | | | - Rajasekaran Ravikesavan
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India; National Institute of Plant Genome Research, New Delhi 110067, India.
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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Srivastava RK, Yadav OP, Kaliamoorthy S, Gupta SK, Serba DD, Choudhary S, Govindaraj M, Kholová J, Murugesan T, Satyavathi CT, Gumma MK, Singh RB, Bollam S, Gupta R, Varshney RK. Breeding Drought-Tolerant Pearl Millet Using Conventional and Genomic Approaches: Achievements and Prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:781524. [PMID: 35463391 PMCID: PMC9021881 DOI: 10.3389/fpls.2022.781524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/11/2022] [Indexed: 06/03/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is a C4 crop cultivated for its grain and stover in crop-livestock-based rain-fed farming systems of tropics and subtropics in the Indian subcontinent and sub-Saharan Africa. The intensity of drought is predicted to further exacerbate because of looming climate change, necessitating greater focus on pearl millet breeding for drought tolerance. The nature of drought in different target populations of pearl millet-growing environments (TPEs) is highly variable in its timing, intensity, and duration. Pearl millet response to drought in various growth stages has been studied comprehensively. Dissection of drought tolerance physiology and phenology has helped in understanding the yield formation process under drought conditions. The overall understanding of TPEs and differential sensitivity of various growth stages to water stress helped to identify target traits for manipulation through breeding for drought tolerance. Recent advancement in high-throughput phenotyping platforms has made it more realistic to screen large populations/germplasm for drought-adaptive traits. The role of adapted germplasm has been emphasized for drought breeding, as the measured performance under drought stress is largely an outcome of adaptation to stress environments. Hybridization of adapted landraces with selected elite genetic material has been stated to amalgamate adaptation and productivity. Substantial progress has been made in the development of genomic resources that have been used to explore genetic diversity, linkage mapping (QTLs), marker-trait association (MTA), and genomic selection (GS) in pearl millet. High-throughput genotyping (HTPG) platforms are now available at a low cost, offering enormous opportunities to apply markers assisted selection (MAS) in conventional breeding programs targeting drought tolerance. Next-generation sequencing (NGS) technology, micro-environmental modeling, and pearl millet whole genome re-sequence information covering circa 1,000 wild and cultivated accessions have helped to greater understand germplasm, genomes, candidate genes, and markers. Their application in molecular breeding would lead to the development of high-yielding and drought-tolerant pearl millet cultivars. This review examines how the strategic use of genetic resources, modern genomics, molecular biology, and shuttle breeding can further enhance the development and delivery of drought-tolerant cultivars.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - O. P. Yadav
- Indian Council of Agricultural Research-Central Arid Zone Research Institute, Jodhpur, India
| | - Sivasakthi Kaliamoorthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Desalegn D. Serba
- United States Department of Agriculture-Agriculture Research Service (ARS), U.S. Arid Land Agricultural Research Center, Maricopa, AZ, United States
| | - Sunita Choudhary
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Tharanya Murugesan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - C. Tara Satyavathi
- Indian Council of Agricultural Research – All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Murali Krishna Gumma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Srikanth Bollam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev Gupta
- United States Department of Agriculture-Agriculture Research Service (ARS), Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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23
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Ndiaye A, Diallo AO, Fall NC, Diouf RD, Diouf D, Kane NA. Transcriptomic analysis of methyl jasmonate treatment reveals gene networks involved in drought tolerance in pearl millet. Sci Rep 2022; 12:5158. [PMID: 35338214 PMCID: PMC8956577 DOI: 10.1038/s41598-022-09152-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
Water deficit stress at the early stage of development is one of the main factors limiting pearl millet production. One practice to counteract this limitation would be to resort to the application of hormones to stimulate plant growth and development at critical stages. Exogenous methyl jasmonate (MeJA) can improve drought tolerance by modulating signaling, metabolism, and photosynthesis pathways, therefore, we assumed that can occur in pearl millet during the early stage of development. To decipher the molecular mechanisms controlling these pathways, RNAseq was conducted in two pearl millet genotypes, drought-sensitive SosatC88 and drought-tolerant Souna3, in response to 200 μM of MeJA. Pairwise comparison between the MeJA-treated and non-treated plants revealed 3270 differentially expressed genes (DEGs) among 20,783 transcripts in SosatC88 and 127 DEGs out of 20,496 transcripts in Souna3. Gene ontology (GO) classification assigned most regulated DEGs in SosatC88 to heme binding, oxidation-reduction process, response to oxidative stress and membrane, and in Souna3 to terpene synthase activity, lyase activity, magnesium ion binding, and thylakoid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis reveals that DEGs in SosatC88 are related to the oxidation-reduction process, the biosynthesis of other secondary metabolites, the signal transduction, and the metabolism of terpenoids, while in Souna3, DEGs are related to the metabolism of terpenoids and the energy metabolism. Two genes encoding a diterpenoid biosynthesis-related (Pgl_GLEAN_10009413) and a Glutathione S transferase T3 (Pgl_GLEAN_10034098) were contra-regulated between SosatC88 and Souna3. Additionally, five random genes differentially expressed by RNAseq were validated using qPCR, therefore, they are potential targets for the development of novel strategies breeding schemes for plant growth under water deficit stress. These insights into the molecular mechanisms of pearl millet genotype tolerance at the early stage of development contribute to the understanding of the role of hormones in adaptation to drought-prone environments.
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Affiliation(s)
- Adama Ndiaye
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal.,Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop (UCAD), 10700, Dakar-Fann, Dakar, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Amadou Oury Diallo
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Ndèye Coura Fall
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal
| | - Rose Diambogne Diouf
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop (UCAD), 10700, Dakar-Fann, Dakar, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Ndjido Ardo Kane
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal. .,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal.
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24
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Vatanen T, Sakwinska O, Wilson B, Combremont S, Cutfield WS, Chan SY, Godfrey KM, O'Sullivan JM. Transcription shifts in gut bacteria shared between mothers and their infants. Sci Rep 2022; 12:1276. [PMID: 35075183 PMCID: PMC8786960 DOI: 10.1038/s41598-022-04848-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023] Open
Abstract
The infant gut microbiome contains a portion of bacteria that originate from the maternal gut. In the infant gut these bacteria encounter a new metabolic environment that differs from the adult gut, consequently requiring adjustments in their activities. We used pilot community RNA sequencing data (metatranscriptomes) from ten mother-infant dyads participating in the NiPPeR Study to characterize bacterial gene expression shifts following mother-to-infant transmission. Maternally-derived bacterial strains exhibited large scale gene expression shifts following the transmission to the infant gut, with 12,564 activated and 14,844 deactivated gene families. The implicated genes were most numerous and the magnitude shifts greatest in Bacteroides spp. This pilot study demonstrates environment-dependent, strain-specific shifts in gut bacteria function and underscores the importance of metatranscriptomic analysis in microbiome studies.
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Affiliation(s)
- Tommi Vatanen
- Liggins Institute, The University of Auckland, Private Bag 102904, Auckland, New Zealand.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - O Sakwinska
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., 1000, Lausanne, Switzerland
| | - B Wilson
- Liggins Institute, The University of Auckland, Private Bag 102904, Auckland, New Zealand
| | - S Combremont
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., 1000, Lausanne, Switzerland
| | - W S Cutfield
- Liggins Institute, The University of Auckland, Private Bag 102904, Auckland, New Zealand
- A Better Start - National Science Challenge, Auckland, New Zealand
| | - S Y Chan
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
| | - K M Godfrey
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Private Bag 102904, Auckland, New Zealand.
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- Brain Research New Zealand, The University of Auckland, Auckland, New Zealand.
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25
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Nergui K, Jin S, Zhao L, Liu X, Xu T, Wei J, Chen X, Yang Y, Li H, Liu Y, Wang Y, Liu J, Zhao T, Li Y, Tang L, Sun R, Wang X, Liu Y, Deng X. Comparative analysis of physiological, agronomic and transcriptional responses to drought stress in wheat local varieties from Mongolia and Northern China. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:23-35. [PMID: 34844115 DOI: 10.1016/j.plaphy.2021.11.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major abiotic stresses that threaten wheat production worldwide, especially in the Mongolian Plateau and adjacent regions. This study aims to find local wheat varieties with high yields and drought resistance at various developmental stages based on agronomic traits and drought resistance indices analysis and explore the underlining molecular mechanisms by transcriptome analysis. Our results revealed that drought stress started at the seedling stage has a greater impact on crop yields. Four types of drought responses were found among the tested varieties. Type 1 and type 2 show low tolerance to drought stress despite high or low yield in control condition, type 3 exhibits high yield under control condition but dropped significantly after drought, and type 4 displays relatively high and stable yields under control and drought conditions. Transcriptome analysis performed with the representative varieties of the four types revealed GO terms and KEGG pathways enriched among drought-triggered differential expressed genes (DEGs). A network containing 18 modules was constructed using weighted gene co-expression analysis (WGCNA). Ten modules were significantly correlated to yield by module-trait correlation, and 3 modules showed Darkhan 144 specific gene expression patterns. C2H2 zinc finger factor-recognized motifs were identified from the promoters of genes in these modules. qRT-PCR confirmed several key DEGs with specific expression patterns and physiological measurements validated the relatively low oxidative damage and high antioxidant capacity in the drought tolerant variety Dankhan 144. These findings provide an important basis for local agriculture and breeding of drought-tolerant high yield wheat varieties.
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Affiliation(s)
- Khandmaa Nergui
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Songsong Jin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Li Zhao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoqiang Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tao Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jun Wei
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiuxiu Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Yang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Hui Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yuanyuan Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jie Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tong Zhao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ling Tang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Runze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaohua Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Li H, Yang M, Zhao C, Wang Y, Zhang R. Physiological and proteomic analyses revealed the response mechanisms of two different drought-resistant maize varieties. BMC PLANT BIOLOGY 2021; 21:513. [PMID: 34736392 PMCID: PMC8567644 DOI: 10.1186/s12870-021-03295-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/26/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Drought stress severely limits maize seedling growth and crop yield. Previous studies have elucidated the mechanisms by which maize acquires drought resistance and contends with water deficiency. However, the link between the physiological and molecular variations among maize cultivars are unknown. Here, physiological and proteomic analyses were conducted to compare the stress responses of two maize cultivars with contrasting drought stress tolerance. RESULTS The physiological analysis showed that the drought-tolerant SD609 maize variety maintains relatively high photochemical efficiency by enhancing its protective cyclic electron flow (CEF) mechanism and antioxidative enzymes activities. Proteomics analysis revealed that 198 and 102 proteins were differentially expressed in SD609 and the drought-sensitive SD902 cultivar, respectively. GO and KEGG enrichments indicated that SD609 upregulated proteins associated with photosynthesis, antioxidants/detoxifying enzymes, molecular chaperones and metabolic enzymes. Upregulation of the proteins related to PSII repair and photoprotection improved photochemical capacity in SD609 subjected to moderate drought stress. In SD902, however, only the molecular chaperones and sucrose synthesis pathways were induced and they failed to protect the impaired photosystem. Further analysis demonstrated that proteins related to the electron transport chain (ETC) and redox homeostasis as well as heat shock proteins (HSPs) may be important in protecting plants from drought stress. CONCLUSIONS Our experiments explored the mechanism of drought tolerance and clarified the interconnections between the physiological and proteomic factors contributing to it. In summary, our findings aid in further understanding of the drought tolerance mechanisms in maize.
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Affiliation(s)
- Hongjie Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mei Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chengfeng Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yifan Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Renhe Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Satyavathi CT, Ambawat S, Khandelwal V, Srivastava RK. Pearl Millet: A Climate-Resilient Nutricereal for Mitigating Hidden Hunger and Provide Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:659938. [PMID: 34589092 PMCID: PMC8475763 DOI: 10.3389/fpls.2021.659938] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/03/2021] [Indexed: 06/03/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal crop after rice, wheat, maize, barley and sorghum. It is widely grown on 30 million ha in the arid and semi-arid tropical regions of Asia and Africa, accounting for almost half of the global millet production. Climate change affects crop production by directly influencing biophysical factors such as plant and animal growth along with the various areas associated with food processing and distribution. Assessment of the effects of global climate changes on agriculture can be helpful to anticipate and adapt farming to maximize the agricultural production more effectively. Pearl millet being a climate-resilient crop is important to minimize the adverse effects of climate change and has the potential to increase income and food security of farming communities in arid regions. Pearl millet has a deep root system and can survive in a wide range of ecological conditions under water scarcity. It has high photosynthetic efficiency with an excellent productivity and growth in low nutrient soil conditions and is less reliant on chemical fertilizers. These attributes have made it a crop of choice for cultivation in arid and semi-arid regions of the world; however, fewer efforts have been made to study the climate-resilient features of pearl millet in comparison to the other major cereals. Several hybrids and varieties of pearl millet were developed during the past 50 years in India by both the public and private sectors. Pearl millet is also nutritionally superior and rich in micronutrients such as iron and zinc and can mitigate malnutrition and hidden hunger. Inclusion of minimum standards for micronutrients-grain iron and zinc content in the cultivar release policy-is the first of its kind step taken in pearl millet anywhere in the world, which can lead toward enhanced food and nutritional security. The availability of high-quality whole-genome sequencing and re-sequencing information of several lines may aid genomic dissection of stress tolerance and provide a good opportunity to further exploit the nutritional and climate-resilient attributes of pearl millet. Hence, more efforts should be put into its genetic enhancement and improvement in inheritance to exploit it in a better way. Thus, pearl millet is the next-generation crop holding the potential of nutritional richness and the climate resilience and efforts must be targeted to develop nutritionally dense hybrids/varieties tolerant to drought using different omics approaches.
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Affiliation(s)
- C. Tara Satyavathi
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Supriya Ambawat
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Vikas Khandelwal
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Rakesh K. Srivastava
- Department of Molecular Breeding (Genomics Trait Discovery), International Crops Research Institute for Semi-arid Tropics, Patancheru, India
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Zhang A, Ji Y, Sun M, Lin C, Zhou P, Ren J, Luo D, Wang X, Ma C, Zhang X, Feng G, Nie G, Huang L. Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage. BMC Genomics 2021; 22:568. [PMID: 34301177 PMCID: PMC8305952 DOI: 10.1186/s12864-021-07888-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought is one of the major environmental stresses resulting in a huge reduction in crop growth and biomass production. Pearl millet (Pennisetum glaucum L.) has excellent drought tolerance, and it could be used as a model plant to study drought resistance. The root is a very crucial part of plant that plays important roles in plant growth and development, which makes it a focus of research. RESULTS In this study, we explored the mechanism of drought tolerance of pearl millet by comparing physiological and transcriptomic data under normal condition and drought treatment at three time points (1 h, 3 h and 7 h) in the root during the seedling stage. The relative electrical conductivity went up from 1 h to 7 h in both control and drought treatment groups while the content of malondialdehyde decreased. A total of 2004, 1538 and 605 differentially expressed genes were found at 1 h, 3 h and 7 h respectively and 12 genes showed up-regulation at all time points. Some of these differentially expressed genes were significantly enriched into 'metabolic processes', 'MAPK signaling pathway' and 'plant hormone signal transduction' such as the ABA signal transduction pathway in GO and KEGG enrichment analysis. CONCLUSIONS Pearl millet was found to have a quick drought response, which may occur before 1 h that contributes to its tolerance against drought stress. These results can provide a theoretical basis to enhance the drought resistance in other plant species.
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Affiliation(s)
- Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puding Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Juncai Ren
- College of Animal Science and Technology, Southwest University, Rongchang Campus, Chongqing, 402460, China
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congyu Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Jogawat A, Yadav B, Lakra N, Singh AK, Narayan OP. Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review. PHYSIOLOGIA PLANTARUM 2021; 172:1106-1132. [PMID: 33421146 DOI: 10.1111/ppl.13328] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/08/2020] [Accepted: 01/01/2021] [Indexed: 05/21/2023]
Abstract
Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.
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Affiliation(s)
| | - Bindu Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nita Lakra
- Department of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Amit Kumar Singh
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Om Prakash Narayan
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts, USA
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Park S, Wijeratne AJ, Moon Y, Waterland NL. Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing. PLoS One 2021; 16:e0250284. [PMID: 33901201 PMCID: PMC8075263 DOI: 10.1371/journal.pone.0250284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Water deficit limits plant growth and development, resulting in quality loss of horticultural crops. However, there is limited information on gene regulation and signaling pathways related to water deficit stress response at multiple time points. The objective of this research was to investigate global gene expression patterns under water deficit stress to provide an insight into how petunia (Petunia ×hybrida 'Mitchell Diploid') responded in the process of stress. Nine-week-old petunias were irrigated daily or placed under water stress by withholding water. Stressed plants reduced stomatal conductance after five days of water deficit, indicating they perceived stress and initiated stress response mechanisms. To analyze transcriptomic changes at the early stage of water deficit, leaf tissue samples were collected 1, 3, and 5 days after water was withheld for RNA sequencing. Under water deficit stress, 154, 3611, and 980 genes were upregulated and 41, 2806, and 253 genes were downregulated on day 1, 3, and 5, respectively. Gene Ontology analysis revealed that redox homeostasis processes through sulfur and glutathione metabolism pathways, and hormone signal transduction, especially abscisic acid and ethylene, were enriched under water deficit stress. Thirty-four transcription factor families were identified, including members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP families, and TFs in AP2/ERF family was the most abundant in petunia. Interestingly, only one member of GRFs was upregulated on day 1, while most of TFs were differentially expressed on day 3 and/or 5. The transcriptome data from this research will provide valuable molecular resources for understanding the early stages of water stress-responsive networks as well as engineering petunia with enhanced water stress tolerance.
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Affiliation(s)
- Suejin Park
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Youyoun Moon
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Nicole L. Waterland
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
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Senevirathna JDM, Asakawa S. Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales. Life (Basel) 2021; 11:364. [PMID: 33923876 PMCID: PMC8074237 DOI: 10.3390/life11040364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 11/25/2022] Open
Abstract
Lipid synthesis pathways of toothed whales have evolved since their movement from the terrestrial to marine environment. The synthesis and function of these endogenous lipids and affecting factors are still little understood. In this review, we focused on different omics approaches and techniques to investigate lipid metabolism and radiation impacts on lipids in toothed whales. The selected literature was screened, and capacities, possibilities, and future approaches for identifying unusual lipid synthesis pathways by omics were evaluated. Omics approaches were categorized into the four major disciplines: lipidomics, transcriptomics, genomics, and proteomics. Genomics and transcriptomics can together identify genes related to unique lipid synthesis. As lipids interact with proteins in the animal body, lipidomics, and proteomics can correlate by creating lipid-binding proteome maps to elucidate metabolism pathways. In lipidomics studies, recent mass spectroscopic methods can address lipid profiles; however, the determination of structures of lipids are challenging. As an environmental stress, the acoustic radiation has a significant effect on the alteration of lipid profiles. Radiation studies in different omics approaches revealed the necessity of multi-omics applications. This review concluded that a combination of many of the omics areas may elucidate the metabolism of lipids and possible hazards on lipids in toothed whales by radiation.
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Affiliation(s)
- Jayan D. M. Senevirathna
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
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Fan Y, Arbab AAI, Zhang H, Yang Y, Lu X, Han Z, Yang Z. MicroRNA-193a-5p Regulates the Synthesis of Polyunsaturated Fatty Acids by Targeting Fatty Acid Desaturase 1 ( FADS1) in Bovine Mammary Epithelial Cells. Biomolecules 2021; 11:biom11020157. [PMID: 33504005 PMCID: PMC7911131 DOI: 10.3390/biom11020157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular diseases (CVDs) are seriously threatening to human life and health. Polyunsaturated fatty acids (PUFAs) are known for their role in preventing CVDs. It is beneficial to population health to promote the content of PUFAs in bovine milk. In recent years, limited research based on molecular mechanisms has focused on this field. The biological roles of numerous microRNAs (miRNAs) remain unknown. In this study, a promising and negatively correlated pair of the miRNA (miRNA-193a-5p) and a fatty acid desaturase 1 (FADS1) gene are identified and screened to explore whether they are potential factors of PUFAs’ synthesis in bovine milk. The targeted relationship between miRNA-193a-5p and FADS1 in bovine mammary epithelial cells (BMECs) is demonstrated by dual luciferase reporter assays. qRT-PCR and western blot assays indicate that both the expression of mRNA and the protein FADS1 show a negative correlation with miRNA-193a-5p expression in BMECs. Also, miR-193a-5p expression is positively correlated with the expression of genes associated with milk fatty acid metabolism, including ELOVL fatty acid elongase 6 (ELOVL6) and diacylglycerol O-acyltransferase 2 (DGAT2). The expression of fatty acid desaturase 2 (FADS2) is negatively correlated with miR-193a-5p expression in BMECs. The contents of triglycerides (TAG), eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA) have a significant positive correlation with the expression of FADS1 and a significant negative correlation with the expression of miR-193a-5p in BMECs. For the first time, this study confirms that miRNA-193a-5p regulates PUFAs metabolism in BMECs by targeting FADS1, indicating that miRNA-193a-5p and FADS1 are underlying factors that improve PUFAs content in bovine milk.
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Affiliation(s)
- Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Abdelaziz Adam Idriss Arbab
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Huimin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yi Yang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ziyin Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (A.A.I.A.); (H.Z.); (X.L.); (Z.H.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-8797-9269
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Dudhate A, Shinde H, Yu P, Tsugama D, Gupta SK, Liu S, Takano T. Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). BMC Genomics 2021; 22:70. [PMID: 33478383 PMCID: PMC7818933 DOI: 10.1186/s12864-021-07382-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/12/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. RESULTS Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (- 073, - 29, and - 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet. CONCLUSION The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
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Affiliation(s)
- Ambika Dudhate
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
- Department of Pharmaceutical Sciences, Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY USA
| | - Harshraj Shinde
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY USA
| | - Pei Yu
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State India
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin’an, Hangzhou China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
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Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
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Shivhare R, Asif MH, Lata C. Comparative transcriptome analysis reveals the genes and pathways involved in terminal drought tolerance in pearl millet. PLANT MOLECULAR BIOLOGY 2020; 103:639-652. [PMID: 32430635 DOI: 10.1007/s11103-020-01015-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/11/2020] [Indexed: 05/09/2023]
Affiliation(s)
- Radha Shivhare
- CSIR- National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mehar H Asif
- CSIR- National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Charu Lata
- CSIR- National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067, India.
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Liu G, Zenda T, Liu S, Wang X, Jin H, Dong A, Yang Y, Duan H. Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize. Genes Genomics 2020; 42:937-955. [PMID: 32623576 DOI: 10.1007/s13258-020-00962-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/21/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Drought is the major abiotic stress factor that negatively influences growth and yield in cereal grain crops such as maize (Zea mays L.). A multitude of genes and pathways tightly modulate plant growth, development and responses to environmental stresses including drought. Therefore, crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought responses. OBJECTIVE Here, we sought to elucidate the molecular and physiological mechanisms underpinning maize drought stress tolerance. METHODS We therefore applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at the late vegetative (V12) growth stage and performed a large-scale RNA sequencing (RNA-seq) transcriptome analysis of the leaf tissues. RESULTS A comparative analysis of the two genotypes leaf transcriptomes and physiological parameters revealed the key differentially expressed genes (DEGs) and metabolic pathways that respond to drought in a genotype-specific manner. A total of 3114 DEGs were identified, with 21 DEGs being specifically expressed in tolerant genotype ND476 in response to drought stress. Of these, genes involved in secondary metabolites biosynthesis, transcription factor regulation, detoxification and stress defense were highly expressed in ND476. Physiological analysis results substantiated our RNA-seq data, with ND476 exhibiting better cell water retention, higher soluble protein content and guaiacol peroxidase activity, along with low lipid peroxidation extent than the sensitive cultivar ZX978 under drought conditions. CONCLUSION Our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Additionally, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.
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Affiliation(s)
- Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China. .,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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K. Srivastava R, Bollam S, Pujarula V, Pusuluri M, Singh RB, Potupureddi G, Gupta R. Exploitation of Heterosis in Pearl Millet: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E807. [PMID: 32605134 PMCID: PMC7412370 DOI: 10.3390/plants9070807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
| | | | | | | | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
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De novo assembly and comparative transcriptome analysis of contrasting pearl millet (Pennisetum glaucum L.) genotypes under terminal drought stress using illumina sequencing. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00324-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Li Q, Xiang C, Xu L, Cui J, Fu S, Chen B, Yang S, Wang P, Xie Y, Wei M, Wang Z. SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum. BMC Genomics 2020; 21:52. [PMID: 31948405 PMCID: PMC6966868 DOI: 10.1186/s12864-019-6441-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022] Open
Abstract
Background Pennisetum giganteum, an abundant, fast-growing perennial C4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a source of forage for cattle and sheep, and as a tool to remedy soil erosion. However, having a chilling-sensitive nature, P. giganteum seedlings need to be protected while overwintering in most temperate climate regions. Results To elucidate the cold stress responses of P. giganteum, we carried out comprehensive full-length transcriptomes from leaf and root tissues under room temperature (RT) and chilling temperature (CT) using PacBio Iso-Seq long reads. We identified 196,124 and 140,766 full-length consensus transcripts in the RT and CT samples, respectively. We then systematically performed functional annotation, transcription factor identification, long non-coding RNAs (lncRNAs) prediction, and simple sequence repeat (SSR) analysis of those full-length transcriptomes. Isoform analysis revealed that alternative splicing events may be induced by cold stress in P. giganteum, and transcript variants may be involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in P. giganteum. Furthermore, the fatty acid composition determination and gene expression level analysis supported that C18 unsaturated fatty acid biosynthesis and metabolism pathways may play roles during cold stress in P. giganteum. Conclusions We provide the first comprehensive full-length transcriptomic resource for the abundant and fast-growing perennial grass Pennisetum giganteum. Our results provide a useful transcriptomic resource for exploring the biological pathways involved in the cold stress responses of P. giganteum.
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Affiliation(s)
- Qingyuan Li
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Conglin Xiang
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lin Xu
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Jinghua Cui
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Shao Fu
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Baolin Chen
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Shoukun Yang
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Pan Wang
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yanfeng Xie
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Ming Wei
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Zhanchang Wang
- Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.
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Fradera-Sola A, Thomas A, Gasior D, Harper J, Hegarty M, Armstead I, Fernandez-Fuentes N. Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PLoS One 2019; 14:e0220518. [PMID: 31361773 PMCID: PMC6667212 DOI: 10.1371/journal.pone.0220518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegrass populations are exposed to a range of environmental conditions and stresses on a seasonal basis and from year to year. One source of potential stress is limitation on water availability. The ability of these perennial grasses to be able to withstand and recover after periods of water limitation or drought can be a key component of grassland performance. Thus, we were interested in looking at changes in patterns of gene expression associated with increasing water stress. Clones of a single genotype of perennial ryegrass were grown under non-flowering growth room conditions in vermiculite supplemented with nutrient solution. Leaf and root tissue was sampled at 4 times in quadruplicate relating to estimated water contents of 35%, 15%, 5% and 1%. RNA was extracted and RNAseq used to generate transcriptome profiles at each sampling point. Transcriptomes were assembled using the published reference genome sequence and differential gene expression analysed using 3 different programmes, DESeq2, edgeR and limma (with the voom transformation), individually and in combination, deriving Early, Middle and Late stage comparisons. Identified differentially expressed genes were then associated with enriched GO terms using BLAST2GO. For the leaf, up-regulated differentially expressed genes were strongly associated with GO terms only during the Early stage and the majority of GO terms were associated with only down-regulated genes at the Middle or Late stages. For the roots, few differentially expressed genes were identified at either Early or Middle stages. Only one replicate at 1% estimated water content produced high quality data for the root, however, this indicated a high level of differential expression. Again the majority of enriched GO terms were associated with down-regulated genes. The performance of the different analysis programmes and the annotations associated with identified differentially expressed genes is discussed.
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Affiliation(s)
- Albert Fradera-Sola
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Ann Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Dagmara Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - John Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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Neji M, Gorel A, Ojeda DI, Duminil J, Kastally C, Steppe K, Fayolle A, Hardy OJ. Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress. Gene 2019; 694:50-62. [PMID: 30716444 DOI: 10.1016/j.gene.2019.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/11/2018] [Accepted: 01/22/2019] [Indexed: 02/01/2023]
Abstract
With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings). Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 up-regulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance.
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Affiliation(s)
- Mohamed Neji
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; Department of Life Sciences, Faculty of Sciences of Gabès, University of Gabès, Tunisia; Laboratory of Extremophile Plants, Centre of Biotechnology of Borj Cedria, Hammam-Lif, Tunisia.
| | - Anais Gorel
- Department Biosystem Engineering (BIOSE), Gembloux Agro-Bio Tech, University of Liege, Belgium
| | - Dario I Ojeda
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; Unit of Ecology and Genetics, Department of Biology, Oulu University, Finland; Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Jérôme Duminil
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium; UMR-DIADE, Institut de Recherche pour le Développement, Univ. Montpellier, Montpellier, France
| | - Chedly Kastally
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Adeline Fayolle
- Department Biosystem Engineering (BIOSE), Gembloux Agro-Bio Tech, University of Liege, Belgium
| | - Olivier J Hardy
- Unit of Evolutionary Biology & Ecology, Faculté des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium
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Zenda T, Liu S, Wang X, Liu G, Jin H, Dong A, Yang Y, Duan H. Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines. Int J Mol Sci 2019; 20:ijms20061268. [PMID: 30871211 PMCID: PMC6470692 DOI: 10.3390/ijms20061268] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R2 = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.
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Affiliation(s)
- Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
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Chaichi M, Sanjarian F, Razavi K, Gonzalez-Hernandez JL. Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity. PLoS One 2019; 14:e0212671. [PMID: 30840683 PMCID: PMC6402654 DOI: 10.1371/journal.pone.0212671] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/07/2019] [Indexed: 11/24/2022] Open
Abstract
In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.
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Affiliation(s)
- Mehrdad Chaichi
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Forough Sanjarian
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
- * E-mail:
| | - Khadijeh Razavi
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Jose L. Gonzalez-Hernandez
- Agronomy, Horticulture and Plant Sciences Dept., South Dakota State University, Brookings, South Dakota, United States of America
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Shinde H, Dudhate A, Tsugama D, Gupta SK, Liu S, Takano T. Pearl millet stress-responsive NAC transcription factor PgNAC21 enhances salinity stress tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:546-553. [PMID: 30447941 DOI: 10.1016/j.plaphy.2018.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 05/07/2023]
Abstract
Pearl millet (Pennisetum glaucum) is the sixth-leading cereal crop and a staple food crop. It is known for its high tolerance to abiotic stress and good nutrient profile. NAC (NAM, ATAF1/2 and CUC) transcription factors (TFs) play an important role in abiotic stress tolerance. In our study, the pearl millet stress-responsive NAC TF gene PgNAC21 was characterized. Gene expression analysis revealed that PgNAC21 expression is induced by salinity stress and abscisic acid (ABA) treatment. In silico promoter analysis showed the presence of ABA response elements (ABREs) and MYB TF binding sites. A yeast one-hybrid assay indicated that a putative MYB TF in pearl millet, PgMYB1, binds to the promoter of PgNAC21. A transactivation assay in yeast cells revealed that PgNAC21 functions as a transcription activator and that its activation domain is located in its C-terminus. Relative to control plants, Arabidopsis plants overexpressing PgNAC21 exhibited better seed germination, heavier fresh weight and greater root length under salinity stress. Overexpression of PgNAC21 in Arabidopsis plants also enhanced the expression of stress-responsive genes such as GSTF6 (GLUTATHIONE S-TRANSFERASE 6), COR47 (COLD-REGULATED 47) and RD20 (RESPONSIVE TO DEHYDRATION 20). Our data demonstrate that PgNAC21 functions as a stress-responsive NAC TF and can be utilized in transgenic approaches for developing salinity stress tolerance in crop plants.
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Affiliation(s)
- Harshraj Shinde
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| | - Ambika Dudhate
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| | - Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo-shi, Hokkaido, Japan.
| | - Shashi K Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India.
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin'an, Hangzhou, China.
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002, Japan.
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Zenda T, Liu S, Wang X, Jin H, Liu G, Duan H. Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms. Int J Mol Sci 2018; 19:E3225. [PMID: 30340410 PMCID: PMC6213998 DOI: 10.3390/ijms19103225] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 01/22/2023] Open
Abstract
Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance.
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Affiliation(s)
- Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
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