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Shu J, Zhang L, Liu G, Wang X, Liu F, Zhang Y, Chen Y. Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes. Int J Mol Sci 2024; 25:2187. [PMID: 38396864 PMCID: PMC10889177 DOI: 10.3390/ijms25042187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/05/2023] [Accepted: 12/30/2023] [Indexed: 02/25/2024] Open
Abstract
Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis-antenna proteins, nitrogen metabolism, plant-pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5'-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance.
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Affiliation(s)
- Jinshuai Shu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing 100081, China; (X.W.); (F.L.); (Y.Z.); (Y.C.)
| | - Lili Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (L.Z.); (G.L.)
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (L.Z.); (G.L.)
| | - Xiaoxuan Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing 100081, China; (X.W.); (F.L.); (Y.Z.); (Y.C.)
| | - Fuzhong Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing 100081, China; (X.W.); (F.L.); (Y.Z.); (Y.C.)
| | - Ying Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing 100081, China; (X.W.); (F.L.); (Y.Z.); (Y.C.)
| | - Yuhui Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing 100081, China; (X.W.); (F.L.); (Y.Z.); (Y.C.)
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Joshi A, Yang SY, Song HG, Min J, Lee JH. Genetic Databases and Gene Editing Tools for Enhancing Crop Resistance against Abiotic Stress. Biology (Basel) 2023; 12:1400. [PMID: 37997999 PMCID: PMC10669554 DOI: 10.3390/biology12111400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
Abiotic stresses extensively reduce agricultural crop production globally. Traditional breeding technology has been the fundamental approach used to cope with abiotic stresses. The development of gene editing technology for modifying genes responsible for the stresses and the related genetic networks has established the foundation for sustainable agriculture against environmental stress. Integrated approaches based on functional genomics and transcriptomics are now expanding the opportunities to elucidate the molecular mechanisms underlying abiotic stress responses. This review summarizes some of the features and weblinks of plant genome databases related to abiotic stress genes utilized for improving crops. The gene-editing tool based on clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized stress tolerance research due to its simplicity, versatility, adaptability, flexibility, and broader applications. However, off-target and low cleavage efficiency hinder the successful application of CRISPR/Cas systems. Computational tools have been developed for designing highly competent gRNA with better cleavage efficiency. This powerful genome editing tool offers tremendous crop improvement opportunities, overcoming conventional breeding techniques' shortcomings. Furthermore, we also discuss the mechanistic insights of the CRISPR/Cas9-based genome editing technology. This review focused on the current advances in understanding plant species' abiotic stress response mechanism and applying the CRISPR/Cas system genome editing technology to develop crop resilience against drought, salinity, temperature, heavy metals, and herbicides.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea;
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
| | - Hyung-Geun Song
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
| | - Jiho Min
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea;
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea; (S.-Y.Y.); (H.-G.S.)
- Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea
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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) 2023; 12:1412. [PMID: 36987099 PMCID: PMC10057621 DOI: 10.3390/plants12061412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Choudhary P, Shukla P, Muthamilarasan M. Genetic enhancement of climate-resilient traits in small millets: A review. Heliyon 2023; 9:e14502. [PMID: 37064482 PMCID: PMC10102230 DOI: 10.1016/j.heliyon.2023.e14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/28/2023] Open
Abstract
Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.
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Shrestha N, Hu H, Shrestha K, Doust AN. Pearl millet response to drought: A review. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Singh M, Nara U. Genetic insights in pearl millet breeding in the genomic era: challenges and prospects. Plant Biotechnol Rep 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Satyavathi CT, Tomar RS, Ambawat S, Kheni J, Padhiyar SM, Desai H, Bhatt SB, Shitap MS, Meena RC, Singhal T, Sankar SM, Singh SP, Khandelwal V. Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]. Sci Rep 2022; 12:276. [PMID: 34997160 PMCID: PMC8742121 DOI: 10.1038/s41598-021-04388-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Pearl millet is an important staple food crop of poor people and excels all other cereals due to its unique features of resilience to adverse climatic conditions. It is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Hence, this is a key to alleviate malnutrition and ensure nutritional security. This study was conducted to identify and validate candidate genes governing grain iron and zinc content enabling the desired modifications in the genotypes. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N50 of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high iron and zinc showed differential gene expression during different stages. Of which, 155 were up-regulated and 251 were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.
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Affiliation(s)
- C Tara Satyavathi
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India.
| | - Rukam S Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Supriya Ambawat
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
| | - Jasminkumar Kheni
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Shital M Padhiyar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Hiralben Desai
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - S B Bhatt
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - M S Shitap
- Department of Agricultural Statistics, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Ramesh Chand Meena
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
| | - Tripti Singhal
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - S Mukesh Sankar
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - S P Singh
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Vikas Khandelwal
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
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12
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Jha S, Maity S, Singh J, Chouhan C, Tak N, Ambatipudi K. Integrated physiological and comparative proteomics analysis of contrasting genotypes of pearl millet reveals underlying salt-responsive mechanisms. Physiol Plant 2022; 174:e13605. [PMID: 34837239 DOI: 10.1111/ppl.13605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/11/2021] [Indexed: 05/20/2023]
Abstract
Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.) with contrasting tolerance for salinity exhibited differential morpho-physiological and proteomic responses under 150 mM NaCl. The genotype IC 325825 was shown to withstand the stress better than IP 17224. The salt-tolerance potential of IC 325825 was associated with its ability to maintain intracellular osmotic, ionic, and redox homeostasis and membrane integrity under stress. The IC 325825 genotype exhibited a higher abundance of C4 photosynthesis enzymes, efficient enzymatic and non-enzymatic antioxidant system, and lower Na+ /K+ ratio compared with IP 17224. Comparative proteomics analysis revealed greater metabolic perturbation in IP 17224 under salinity, in contrast to IC 325825 that harbored pro-active stress-responsive machinery, allowing its survival and better adaptability under salt stress. The differentially abundant proteins were in silico characterized for their functions, subcellular-localization, associated pathways, and protein-protein interaction. These proteins were mainly involved in photosynthesis/response to light stimulus, carbohydrate and energy metabolism, and stress responses. Proteomics data were validated through expression profiling of the selected genes, revealing a poor correlation between protein abundance and their relative transcript levels. This study has provided novel insights into salt adaptive mechanisms in P. glaucum, demonstrating the power of proteomics-based approaches. The critical proteins identified in the present study could be further explored as potential objects for engineering stress tolerance in salt-sensitive major crops.
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Affiliation(s)
- Shweta Jha
- Plant Functional Genomics Lab, Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, India
| | - Sudipa Maity
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Jawahar Singh
- Plant Functional Genomics Lab, Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, India
| | - Chaya Chouhan
- Plant Functional Genomics Lab, Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, India
| | - Nisha Tak
- BNF and Microbial Genomics Lab, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, India
| | - Kiran Ambatipudi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Akinduti P, Obafemi YD, Isibor PO, Ishola R, Ahuekwe FE, Ayodele OA, Oduleye OS, Oziegbe O, Onagbesan OM. Antibacterial kinetics and phylogenetic analysis of Aloe vera plants. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.6526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Uncontrolled use of antibiotics has resulted in the emergence of resistant bacteria. It has necessitated the evaluation of antibacterial activities and phylo-diversity of Aloe vera (also called Aloe barbadensis) plants as antimicrobial agent in Nigeria. Biotyped enteric bacilli of 251 strains obtained from fecal samples of patients with various gastro-intestinal complications are profiled for antibiogram. Resistant biotypes were assayed for susceptibility to Aloe vera latex and further evaluated for time-kill kinetics and phylo-diversity. More than 30% of enteric bacilli, including Citrobacter freundii, Escherichia coli and Proteus mirabilis were resistant to cotrimoxazole, ciprofloxacin, and tetracycline respectively at MIC >16 µg/ml (p=0.004). Aloe vera latex significantly inhibited 39.5% resistant enteric biotypes with a significant average reduction of the viable count at 1xMIC and 2xMIC to less than 3.0 Log10CFU/mL after 24 hours. Flavonoids, alkaloids, terpenoids and anthraquinine in anti-enteric sap significantly correlated and regressed with antibacterial activity (p<0.05), while two of the antimicrobial Aloe vera plants showed phylogenetic relatedness with other homologous. Anti-bacteria efficacy of some Nigerian Aloe vera latex could provide alternative therapy, while its phylo-diversity and genomic profiling would offer a promising avenue for identification and development of antimicrobial agents as drug candidates for natural antibiotics.
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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. Front Plant Sci 2021; 12:659938. [PMID: 34589092 PMCID: PMC8475763 DOI: 10.3389/fpls.2021.659938] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Miao G, Qin Y, Guo J, Zhang Q, Bao Y. Transcriptome characterization and expression profile of Coix lacryma-jobi L. in response to drought. PLoS One 2021; 16:e0256875. [PMID: 34478459 PMCID: PMC8415600 DOI: 10.1371/journal.pone.0256875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Coix lacryma-jobi L. is a very important economic crop widely cultivated in Southeast Asia. Drought affects more than four million square kilometers every year, and is a significant factor limiting agricultural productivity. However, relatively little is known about how Coix lacryma-jobi L. responds to drought treatments. To obtain a detailed and comprehensive understanding of the mechanisms regulating the transcriptional responses of Coix lacryma-jobi L. to drought treatment, we employed high throughput short-read sequencing of cDNA prepared from polyadenylated RNA to explore global gene expression after a seven-day drought treatment. We generated a de novo assembled transcriptome comprising 65,480 unique sequences. Differential expression analysis based on RSEM-estimated transcript abundances identified 5,315 differentially expressed genes (DEGs) when comparing samples from plants following drought-treatment and from the appropriate controls. Among these, the transcripts for 3,460 genes were increased in abundance, whereas 1,855 were decreased. Real-time quantitative PCR for 5 transcripts confirmed the changes identified by RNA-Seq. The results provide a transcriptional overview of the changes in Coix lacryma-jobi L. in response to drought, and will be very useful for studying the function of associated genes and selection of molecular marker of Coix lacryma-jobi L in the future.
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Affiliation(s)
- Guidong Miao
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, Guizhou Province, China
- * E-mail:
| | - Yan Qin
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, Guizhou Province, China
| | - Jihua Guo
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, Guizhou Province, China
| | - Qingxia Zhang
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, Guizhou Province, China
| | - Yingying Bao
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, Guizhou Province, China
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Negi A, George Kokkat J, Jasrotia RS, Madhavan S, Jaiswal S, Angadi UB, Iquebal MA, Kalathil Palliyarakkal M, Palaniyandi U, Rai A, Kumar D. Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web-genomic resource. Physiol Plant 2021; 172:669-683. [PMID: 33305409 DOI: 10.1111/ppl.13308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Black pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought-affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine-rich repeats and ubiquitin-like domain), serine threonine protein kinase, Mitogen-activated protein kinase, Nucleotide Binding Site-Leucine Rich Repeat, Myeloblastosis-related proteins, basic helix-loop-helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http://webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop drought-tolerant variety for better black pepper productivity.
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Affiliation(s)
- Ankita Negi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Johnson George Kokkat
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Rahul S Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Soumya Madhavan
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa Basavanneppa Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Umadevi Palaniyandi
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
- RBGRC, ICAR-IARI Regional Centre, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chakraborty A, Viswanath A, Malipatil R, Rathore A, Thirunavukkarasu N. Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance. Front Genet 2020; 11:608421. [PMID: 33363575 PMCID: PMC7753210 DOI: 10.3389/fgene.2020.608421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.
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Affiliation(s)
- Animikha Chakraborty
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Abhishek Rathore
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, 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 Mol Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shivhare R, Lakhwani D, Asif MH, Chauhan PS, Lata C. De novo assembly and comparative transcriptome analysis of contrasting pearl millet (Pennisetum glaucum L.) genotypes under terminal drought stress using illumina sequencing. Nucleus 2020; 63:341-52. [DOI: 10.1007/s13237-020-00324-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Chanwala J, Satpati S, Dixit A, Parida A, Giri MK, Dey N. Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress. BMC Genomics 2020; 21:231. [PMID: 32171257 PMCID: PMC7071642 DOI: 10.1186/s12864-020-6622-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/25/2020] [Indexed: 01/19/2023] Open
Abstract
Background Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF family are well known for their role in plant development, phytohormone signaling and developing resistance against biotic or abiotic stresses. In this study, we performed a genome-wide screening to identify and analyze the WRKY TFs in pearl millet (Pennisetum glaucum; PgWRKY), which is one of the most widely grown cereal crops in the semi-arid regions. Results A total number of 97 putative PgWRKY proteins were identified and classified into three major Groups (I-III) based on the presence of WRKY DNA binding domain and zinc-finger motif structures. Members of Group II have been further subdivided into five subgroups (IIa-IIe) based on the phylogenetic analysis. In-silico analysis of PgWRKYs revealed the presence of various cis-regulatory elements in their promoter region like ABRE, DRE, ERE, EIRE, Dof, AUXRR, G-box, etc., suggesting their probable involvement in growth, development and stress responses of pearl millet. Chromosomal mapping evidenced uneven distribution of identified 97 PgWRKY genes across all the seven chromosomes of pearl millet. Synteny analysis of PgWRKYs established their orthologous and paralogous relationship among the WRKY gene family of Arabidopsis thaliana, Oryza sativa and Setaria italica. Gene ontology (GO) annotation functionally categorized these PgWRKYs under cellular components, molecular functions and biological processes. Further, the differential expression pattern of PgWRKYs was noticed in different tissues (leaf, stem, root) and under both drought and salt stress conditions. The expression pattern of PgWRKY33, PgWRKY62 and PgWRKY65 indicates their probable involvement in both dehydration and salinity stress responses in pearl millet. Conclusion Functional characterization of identified PgWRKYs can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions. Further, these PgWRKYs can be employed in genome editing for millet crop improvement.
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Affiliation(s)
- Jeky Chanwala
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Suresh Satpati
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Anshuman Dixit
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Mrunmay Kumar Giri
- School of Biotechnology, Campus 11, KIIT (Deemed to be) University, Patia, Bhubaneswar, Odisha, 751024, India.
| | - Nrisingha Dey
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
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Abstract
Minor and pseudo-cereals, which can grow with lower input and often produce specific nutrients compared to major cereal crops, are attracting worldwide attention. Since these crops generally have a large genetic diversity in a breeding population, rapid genetic improvement can be possible by the application of genomics-assisted breeding methods. In this review, we discuss studies related to biparental quantitative trait locus (QTL) mapping, genome-wide association study, and genomic selection for minor and pseudo-cereals. Especially, we focus on the current progress in a pseudo-cereal, buckwheat. Prospects for the practical utilization of genomics-assisted breeding in minor and pseudo-cereals are discussed including the issues to overcome especially for these crops.
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Affiliation(s)
- Shiori Yabe
- Institute of Crop Science, NARO, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657 Japan
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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: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Su X, Zhao Y, Wang H, Li G, Cheng X, Jin Q, Cai Y. Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis. BMC Plant Biol 2019; 19:417. [PMID: 31604417 PMCID: PMC6788021 DOI: 10.1186/s12870-019-2046-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/20/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. RESULTS In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. CONCLUSIONS Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Han Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
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You J, Zhang Y, Liu A, Li D, Wang X, Dossa K, Zhou R, Yu J, Zhang Y, Wang L, Zhang X. Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress. BMC Plant Biol 2019; 19:267. [PMID: 31221078 PMCID: PMC6585049 DOI: 10.1186/s12870-019-1880-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/10/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes. RESULTS Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame. CONCLUSION The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.
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Affiliation(s)
- Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100 China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiao Wang
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430062 China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, 3320 Sénégal
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Parvathi MS, Nataraja KN, Nanja Reddy YA, Naika MBN, Channabyre Gowda MV. Transcriptome analysis of finger millet ( Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes. J Genet 2019; 98:46. [PMID: 31204698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Finger millet (Eleusine coracana (L.) Gaertn.), an important C4 species is known for its stress hardiness and nutritional significance. To identify novel drought responsive mechanisms, we generated transcriptome data from leaf tissue of finger millet, variety GPU-28, exposed to gravimetrically imposed drought stress so as to simulate field stress conditions. De novo assembly based approach yielded 80,777 and 90,830 transcripts from well-irrigated (control) and drought-stressed samples, respectively. A total of 1790 transcripts were differentially expressed between the control and drought-stress treatments. Functional annotation and pathway analysis indicated activation of diverse drought-stress signalling cascade genes such as serine threonine protein phosphatase 2A (PP2A), calcineurin B-like interacting protein kinase31 (CIPK31), farnesyl pyrophosphate synthase (FPS), signal recognition particle receptor α (SRPR α) etc. The basal regulatory genes such as TATA-binding protein (TBP)-associated factors (TAFs) werefound to be drought responsive, indicating that genes associated with housekeeping or basal regulatory processes are activated underdrought in finger millet. A significant portion of the expressed genes was uncharacterized, belonging to the category of proteins of unknown functions (PUFs). Among the differentially expressed PUFs, we attempted to assign putative function for a few, using anovel annotation tool, Proteins of Unknown Function Annotation Server. Analysis of PUFs led to the discovery of novel drought responsive genes such as pentatricopeptide repeat proteins and tetratricopeptide repeat proteins that serve as interaction modules in multiprotein interactions. The transcriptome data generated can be utilized for comparative analysis, and functional validation of the genes identified would be useful to understand the drought adaptive mechanisms operating under field conditions in finger millet, as has been already attempted for a few candidates such as CIPK31 and TAF6. Such an attempt is needed to enhance the productivity of finger millet under water-limited conditions, and/or to adopt the implicated mechanisms in other related crops.
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Affiliation(s)
- M S Parvathi
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India.
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Woldesemayat AA, Ntwasa M. Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum ( Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses. Front Genet 2018; 9:557. [PMID: 30515190 PMCID: PMC6255970 DOI: 10.3389/fgene.2018.00557] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/31/2018] [Indexed: 12/01/2022] Open
Abstract
Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes. Their interaction network would provide insight into understanding the molecular mechanisms of drought tolerance and underpinning signal pathways. Functional analysis was undertaken to determine significantly enriched genesets for pathways involved in drought tolerance. Analysis of distinct pathway cross-talk network was performed and drought-specific subnetwork was extracted. Investigation of various data sources such as gene expression, regulatory pathways, sorghumCyc, sorghum protein-protein interaction (PPI) and Gene Ontology (GO) revealed 14 major drought stress related hub genes (DSRhub genes). Significantly enriched genesets have shown association with various biological processes underlying drought-related responses. Key metabolic pathways were significantly enriched in the drought-related genes. Systematic analysis of pathways cross-talk and gene interaction network revealed major cross-talk pathway modules associated with drought tolerance. Further investigation of the major DSRhub genes revealed distinct regulatory genes such as ZEP, NCED, AAO, and MCSU and CYP707A1. These were involved in the regulation of ABA biosynthesis and signal transduction. Other protein families, namely, aldehyde and alcohol dehydrogenases, mitogene activated protein kinases (MAPKs), and Ribulose-1,5-biphosphate carboxylase (RuBisCO) were shown to be involved in the drought-related responses. This shows a diversity of complex functional features in sorghum to respond to various abiotic stresses. Finally, we constructed a drought-specific subnetwork, characterized by unique candidate genes that were associated with DSRhub genes. According to our knowledge, this is the first in sorghum drought investigation that introduces pathway and network-based candidate gene approach for analysis of drought tolerance. We provide novel information about pathways cross-talk and signaling networks used in further systems level analysis for understanding the molecular mechanism behind drought tolerance and can, therefore, be adapted to other model and non-model crops.
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Affiliation(s)
- Adugna Abdi Woldesemayat
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, South Africa
| | - Monde Ntwasa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, South Africa
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