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Singh S, Viswanath A, Chakraborty A, Narayanan N, Malipatil R, Jacob J, Mittal S, Satyavathi TC, Thirunavukkarasu N. Identification of key genes and molecular pathways regulating heat stress tolerance in pearl millet to sustain productivity in challenging ecologies. FRONTIERS IN PLANT SCIENCE 2024; 15:1443681. [PMID: 39239194 PMCID: PMC11374647 DOI: 10.3389/fpls.2024.1443681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Pearl millet is a nutri-cereal that is mostly grown in harsh environments, making it an ideal crop to study heat tolerance mechanisms at the molecular level. Despite having a better-inbuilt tolerance to high temperatures than other crops, heat stress negatively affects the crop, posing a threat to productivity gain. Hence, to understand the heat-responsive genes, the leaf and root samples of two contrasting pearl millet inbreds, EGTB 1034 (heat tolerant) and EGTB 1091 (heat sensitive), were subjected to heat-treated conditions and generated genome-wide transcriptomes. We discovered 13,464 differentially expressed genes (DEGs), of which 6932 were down-regulated and 6532 up-regulated in leaf and root tissues. The pairwise analysis of the tissue-based transcriptome data of the two genotypes demonstrated distinctive genotype and tissue-specific expression of genes. The root exhibited a higher number of DEGs compared to the leaf, emphasizing different adaptive strategies of pearl millet. A large number of genes encoding ROS scavenging enzymes, WRKY, NAC, enzymes involved in nutrient uptake, protein kinases, photosynthetic enzymes, and heat shock proteins (HSPs) and several transcription factors (TFs) involved in cross-talking of temperature stress responsive mechanisms were activated in the stress conditions. Ribosomal proteins emerged as pivotal hub genes, highly interactive with key genes expressed and involved in heat stress response. The synthesis of secondary metabolites and metabolic pathways of pearl millet were significantly enriched under heat stress. Comparative synteny analysis of HSPs and TFs in the foxtail millet genome demonstrated greater collinearity with pearl millet compared to proso millet, rice, sorghum, and maize. In this study, 1906 unannotated DEGs were identified, providing insight into novel participants in the molecular response to heat stress. The identified genes hold promise for expediting varietal development for heat tolerance in pearl millet and similar crops, fostering resilience and enhancing grain yield in heat-prone environments.
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Affiliation(s)
- Swati Singh
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Animikha Chakraborty
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Neha Narayanan
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Jinu Jacob
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Shikha Mittal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Tara C Satyavathi
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Global Center of Excellence on Millets (Shree Anna), ICAR-Indian Institute of Millets Research, Hyderabad, India
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Hou Y, Li Q, Zhou H, Kafle S, Li W, Tan L, Liang J, Meng L, Xin H. SMRT sequencing of a full-length transcriptome reveals cold induced alternative splicing in Vitis amurensis root. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108863. [PMID: 38917739 DOI: 10.1016/j.plaphy.2024.108863] [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: 03/02/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Alternative splicing enhances diversity at the transcriptional and protein levels that widely involved in plant response to biotic and abiotic stresses. V. amurensis is an extremely cold-tolerant wild grape variety, however, studies on alternative splicing (AS) in amur grape at low temperatures are currently poorly understood. In this study, we analyzed full-length transcriptome and RNA seq data at 0, 2, and 24 h after cold stress in V. amurensis roots. Following quality control and correction, 221,170 high-quality full-length non-concatemer (FLNC) reads were identified. A total of 16,181 loci and 30,733 isoforms were identified. These included 22,868 novel isoforms from annotated genes and 2815 isoforms from 2389 novel genes. Among the distinguished novel isoforms, 673 Long non-coding RNAs (LncRNAs) and 18,164 novel isoforms open reading frame (ORF) region were found. A total of 2958 genes produced 8797 AS events, of which 189 genes were involved in the low-temperature response. Twelve transcription factors show AS during cold treatment and VaMYB108 was selected for initial exploration. Two transcripts, Chr05.63.1 (VaMYB108short) and Chr05.63.2 (VaMYB108normal) of VaMYB108, display up-regulated expression after cold treatment in amur grape roots and are both localized in the nucleus. Only VaMYB108normal exhibits transcriptional activation activity. Overexpression of either VaMYB108short or VaMYB108normal in grape roots leads to increased expression of the other transcript and both increased chilling resistance of amur grape roots. The results improve and supplement the genome annotations and provide insights for further investigation into AS mechanisms during cold stress in V. amurensis.
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Affiliation(s)
- Yujun Hou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyun Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Subash Kafle
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjuan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lisha Tan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju Liang
- Turpan Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Lin Meng
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haiping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Wang YH, Ye X, Zhao BY, Wang WJ, Zhou ZF, Zhang XQ, Du J, Song JL, Huang XL, Ouyang KX, Zhong TX, Liao FX. Comprehensive analysis of B3 family genes in pearl millet ( Pennisetum glaucum) and the negative regulator role of PgRAV-04 in drought tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1400301. [PMID: 39135652 PMCID: PMC11317251 DOI: 10.3389/fpls.2024.1400301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024]
Abstract
Introduction Members of the plant-specific B3 transcription factor superfamily play crucial roles in various plant growth and developmental processes. Despite numerous valuable studies on B3 genes in other species, little is known about the B3 superfamily in pearl millet. Methods and results Here, through comparative genomic analysis, we identified 70 B3 proteins in pearl millet and categorized them into four subfamilies based on phylogenetic affiliations: ARF, RAV, LAV, and REM. We also mapped the chromosomal locations of these proteins and analyzed their gene structures, conserved motifs, and gene duplication events, providing new insights into their potential functional interactions. Using transcriptomic sequencing and real-time quantitative PCR, we determined that most PgB3 genes exhibit upregulated expression under drought and high-temperature stresses, indicating their involvement in stress response regulation. To delve deeper into the abiotic stress roles of the B3 family, we focused on a specific gene within the RAV subfamily, PgRAV-04, cloning it and overexpressing it in tobacco. PgRAV-04 overexpression led to increased drought sensitivity in the transgenic plants due to decreased proline levels and peroxidase activity. Discussion This study not only adds to the existing body of knowledge on the B3 family's characteristics but also advances our functional understanding of the PgB3 genes in pearl millet, reinforcing the significance of these factors in stress adaptation mechanisms.
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Affiliation(s)
- Yin-Hua Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Xing Ye
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Bi-Yao Zhao
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Wen-Jing Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zheng-Feng Zhou
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, China
| | - Juan Du
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, United States
| | - Jian-Ling Song
- College of biology and chemistry, Minzu Normal University of Xingyi, Xingyi, China
| | - Xiao-Ling Huang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Kun-Xi Ouyang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Tian-Xiu Zhong
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Fei-Xiong Liao
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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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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Kong D, Ma H, Zhu C, Hao Y, Li C. Unraveling the toxicity response and metabolic compensation mechanism of tannic acid-Cr(III) complex on alga Raphidocelis subcapitata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172034. [PMID: 38657806 DOI: 10.1016/j.scitotenv.2024.172034] [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: 01/22/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Due to their assembly properties and variable molecular weights, the potential biological toxicity effects of macromolecular organic ligand heavy metal complexes are more difficult to predict and their mechanisms are more complex. This study unraveled the toxicity response and metabolic compensation mechanism of tannic acid-Cr(III) (TA-Cr(III)) complex on alga Raphidocelis subcapitata using multi-omics approaches. Results showed TA-Cr(III) complex caused oxidative damage and photosystem disruption, destroying the cell morphology and inhibiting algal growth by >80 % at high exposure levels. TA-Cr(III) complex stress down-regulated proteins linked to proliferation, photosynthesis and antioxidation while upregulating carbon fixation, TCA cycle and amino acid metabolism. The increase of fumarate, citrate, isocitrate and semialdehyde succinate was validated by metabolomics analysis, which improved the TCA cycle, amino acid metabolism and carbon fixation. Activation of the above cellular processes somewhat compensated for the inhibition of algal photosynthesis by TA-Cr(III) complex exposure. In conclusion, physiological toxicity coupled with downstream metabolic compensation in response to Cr(III) complex of macromolecular was characterized in Raphidocelis subcapitata, unveiling the adaptive mechanism of algae under the stress of heavy metal complexes with macromolecular organic ligands.
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Affiliation(s)
- Deyi Kong
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi 'an 710021, PR China
| | - Hongrui Ma
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi 'an 710021, PR China.
| | - Chao Zhu
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi 'an 710021, PR China
| | - Yongyong Hao
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi 'an 710021, PR China
| | - Chengtao Li
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi 'an 710021, PR China
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Zhang P, Wang B, Guo Y, Wang T, Wei Q, Luo Y, Li H, Wu H, Wang X, Zhang X. Identification of Drought-Resistant Response in Proso Millet ( Panicum miliaceum L.) Root through Physiological and Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1693. [PMID: 38931125 PMCID: PMC11207614 DOI: 10.3390/plants13121693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Proso millet (Panicum miliaceum L.) is resilient to abiotic stress, especially to drought. However, the mechanisms by which its roots adapt and tolerate salt stress are obscure. In this study, to clarify the molecular mechanism of proso millet in response to drought stress, the physiological indexes and transcriptome in the root of seedlings of the proso millet cultivar 'Yumi 2' were analyzed at 0, 0.5, 1.0, 1.5, and 3.0 h of stimulated drought stress by using 20% PEG-6000 and after 24 h of rehydration. The results showed that the SOD activity, POD activity, soluble protein content, MDA, and O2-· content of 'Yumi 2' increased with the time of drought stress, but rapidly decreased after rehydration. Here, 130.46 Gb of clean data from 18 samples were obtained, and the Q30 value of each sample exceeded 92%. Compared with 0 h, the number of differentially expressed genes (DEGs) reached the maximum of 16,105 after 3 h of drought, including 9153 upregulated DEGs and 6952 downregulated DEGs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that upregulated DEGs were mainly involved in ATP binding, nucleus, protein serine/threonine phosphatase activity, MAPK signaling pathway-plant, plant-pathogen interactions, and plant hormone signal transduction under drought stress, while downregulated DEGs were mainly involved in metal ion binding, transmembrane transporter activity, and phenylpropanoid biosynthesis. Additionally, 1441 TFs screened from DEGs were clustered into 64 TF families, such as AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, and bZIP TF families. Genes related to physiological traits were closely related to starch and sucrose metabolism, phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. In conclusion, the active oxygen metabolism system and the soluble protein of proso millet root could be regulated by the activity of protein serine/threonine phosphatase. AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, and bZIP TF families were found to be closely associated with drought tolerance in proso millet root. This study will provide data to support a subsequent study on the function of the drought tolerance gene in proso millet.
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Affiliation(s)
- Panpan Zhang
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
- Dryland Agricultural Engineering Technology Research Center in Northern of Shaanxi, Yulin 719000, China
| | - Binglei Wang
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Yaning Guo
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
- Dryland Agricultural Engineering Technology Research Center in Northern of Shaanxi, Yulin 719000, China
| | - Tao Wang
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Qian Wei
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Yan Luo
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Hao Li
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Huiping Wu
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
| | - Xiaolin Wang
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
- Dryland Agricultural Engineering Technology Research Center in Northern of Shaanxi, Yulin 719000, China
| | - Xiong Zhang
- College of Life Science, Yulin University, Yulin 719000, China; (B.W.); (Y.G.); (T.W.); (Q.W.); (Y.L.); (H.L.); (H.W.); (X.W.)
- Dryland Agricultural Engineering Technology Research Center in Northern of Shaanxi, Yulin 719000, 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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Ye J, Fan Y, Zhang H, Teng W, Teng K, Wu J, Fan X, Wang S, Yue Y. Octoploids Show Enhanced Salt Tolerance through Chromosome Doubling in Switchgrass ( Panicum virgatum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1383. [PMID: 38794454 PMCID: PMC11124981 DOI: 10.3390/plants13101383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Polyploid plants often exhibit enhanced stress tolerance. Switchgrass is a perennial rhizomatous bunchgrass that is considered ideal for cultivation in marginal lands, including sites with saline soil. In this study, we investigated the physiological responses and transcriptome changes in the octoploid and tetraploid of switchgrass (Panicum virgatum L. 'Alamo') under salt stress. We found that autoploid 8× switchgrass had enhanced salt tolerance compared with the amphidiploid 4× precursor, as indicated by physiological and phenotypic traits. Octoploids had increased salt tolerance by significant changes to the osmoregulatory and antioxidant systems. The salt-treated 8× Alamo plants showed greater potassium (K+) accumulation and an increase in the K+/Na+ ratio. Root transcriptome analysis for octoploid and tetraploid plants with or without salt stress revealed that 302 upregulated and 546 downregulated differentially expressed genes were enriched in genes involved in plant hormone signal transduction pathways and were specifically associated with the auxin, cytokinin, abscisic acid, and ethylene pathways. Weighted gene co-expression network analysis (WGCNA) detected four significant salt stress-related modules. This study explored the changes in the osmoregulatory system, inorganic ions, antioxidant enzyme system, and the root transcriptome in response to salt stress in 8× and 4× Alamo switchgrass. The results enhance knowledge of the salt tolerance of artificially induced homologous polyploid plants and provide experimental and sequencing data to aid research on the short-term adaptability and breeding of salt-tolerant biofuel plants.
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Affiliation(s)
- Jiali Ye
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yupu Fan
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Hui Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Wenjun Teng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Ke Teng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Juying Wu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Xifeng Fan
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
| | - Shiwen Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yuesen Yue
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Y.); (Y.F.); (H.Z.); (W.T.); (K.T.); (J.W.); (X.F.)
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9
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Prusty A, Panchal A, Singh RK, Prasad M. Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review. PLANTA 2024; 259:118. [PMID: 38592589 DOI: 10.1007/s00425-024-04394-2] [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: 12/30/2023] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.
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Affiliation(s)
- Ankita Prusty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- Department of Botany, Mahishadal Raj College, Purba Medinipur, Garh Kamalpur, West Bengal, 721628, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Genetics, University of Delhi, South Campus, Benito-Juarez Road, New Delhi, 110021, India.
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10
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Shen B, Li W, Zheng Y, Zhou X, Zhang Y, Qu M, Wang Y, Yuan Y, Pang K, Feng Y, Wu J, Zeng B. Morphological and molecular response mechanisms of the root system of different Hemarthria compressa species to submergence stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1342814. [PMID: 38638357 PMCID: PMC11024365 DOI: 10.3389/fpls.2024.1342814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Introduction The severity of flood disasters is increasing due to climate change, resulting in a significant reduction in the yield and quality of forage crops worldwide. This poses a serious threat to the development of agriculture and livestock. Hemarthria compressa is an important high-quality forage grass in southern China. In recent years, frequent flooding has caused varying degrees of impacts on H. compressa and their ecological environment. Methods In this study, we evaluated differences in flooding tolerance between the root systems of the experimental materials GY (Guang Yi, flood-tolerant) and N1291 (N201801291, flood-sensitive). We measured their morphological indexes after 7 d, 14 d, and 21 d of submergence stress and sequenced their transcriptomes at 8 h and 24 h, with 0 h as the control. Results During submergence stress, the number of adventitious roots and root length of both GY and N1291 tended to increase, but the overall growth of GY was significantly higher than that of N1291. RNA-seq analysis revealed that 6046 and 7493 DEGs were identified in GY-8h and GY-24h, respectively, and 9198 and 4236 DEGs in N1291-8h and N1291-24h, respectively, compared with the control. The GO and KEGG enrichment analysis results indicated the GO terms mainly enriched among the DEGs were oxidation-reduction process, obsolete peroxidase reaction, and other antioxidant-related terms. The KEGG pathways that were most significantly enriched were phenylpropanoid biosynthesis, plant hormone signal transduction etc. The genes of transcription factor families, such as C2H2, bHLH and bZIP, were highly expressed in the H. compressa after submergence, which might be closely related to the submergence adaptive response mechanisms of H. compressa. Discussion This study provides basic data for analyzing the molecular and morphological mechanisms of H. compressa in response to submergence stress, and also provides theoretical support for the subsequent improvement of submergence tolerance traits of H. compressa.
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Affiliation(s)
- Bingna Shen
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wenwen Li
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yuqian Zheng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiaoli Zhou
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yinuo Zhang
- College of Grassland Agriculture, Northwest Agriculture and Forestry University, Shanxi, China
| | - Minghao Qu
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Institute of Prataculture, Chongqing Academy of Animal Science, Chongqing, China
| | - Yinchen Wang
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Provincial Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou, China
| | - Yang Yuan
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Provincial Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou, China
| | - Kaiyue Pang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yanlong Feng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Jiahai Wu
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Provincial Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
- College of Animal Science and Technology, Southwest University, Chongqing University Herbivore Engineering Research Center, Chongqing, China
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11
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Li J, Li X, Zhang C, Zhou Q, Chen S. Phylogeographic analysis reveals extensive genetic variation of native grass Elymus nutans (Poaceae) on the Qinghai-Tibetan plateau. FRONTIERS IN PLANT SCIENCE 2024; 15:1349641. [PMID: 38529066 PMCID: PMC10961384 DOI: 10.3389/fpls.2024.1349641] [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: 12/05/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024]
Abstract
Introduction Elymus nutans holds ecological and pastoral significance due to its adaptability and nutritional value, the Qinghai-Tibet Plateau (QTP) is a key hub for its genetic diversity. To conserve and harness its genetic resources in highland ecosystems, a thorough assessment is vital. However, a comprehensive phylogeographic exploration of E. nutans is lacking. The objective of this study was to unravel the genetic diversity, adaptation, and phylogenetics of E. nutans populations. Methods Encompassing 361 individuals across 35 populations, the species' genetic landscape and dynamic responses to diverse environments were decoded by using four chloroplast DNA (cpDNA) sequences and nine microsatellite markers derived from the transcriptome. Results and discussion This study unveiled a notable degree of genetic diversity in E. nutans populations at nuclear (I = 0.46, He = 0.32) and plastid DNA levels (Hd = 0.805, π = 0.67). Analysis via AMOVA highlighted genetic variation predominantly within populations. Despite limited isolation by distance (IBD), the Mekong-Salween Divide (MSD) emerged as a significant factor influencing genetic differentiation and conserving diversity. Furthermore, correlations were established between external environmental factors and effective alleles of three EST-SSRs (EN5, EN57 and EN80), potentially linked to glutathione S-transferases T1 or hypothetical proteins, affecting adaptation. This study deepens the understanding of the intricate relationship between genetic diversity, adaptation, and environmental factors within E. nutans populations on the QTP. The findings shed light on the species' evolutionary responses to diverse ecological conditions and contribute to a broader comprehension of plant adaptation mechanisms.
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Affiliation(s)
- Jin Li
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Xinda Li
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Changbing Zhang
- Institute of Grass Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Shiyong Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
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12
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Shokri-Gharelo R, Derakhti-Dizaji M, Dadashi D, Chalekaei M, Rostami-Tobnag G. Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses. Biosystems 2024; 237:105165. [PMID: 38430956 DOI: 10.1016/j.biosystems.2024.105165] [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: 10/30/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Abiotic stresses are predominant and main causes of the losses in the crop yield. A complexity of systems biology and involvement of numerous genes in the response to abiotic factors have challenged efforts to create tolerant cultivars with sustainable production. The root is the main organ of the plant and determines a plant tolerance under stressful conditions. In this study, we carried out a meta-analysis of expression datasets from wheat root to identify differentially expressed genes, followed by the weighted gene co-expression network analysis (WGCNA) to construct the weighted gene co-expression network. The aim was to identify consensus differentially expressed genes with regulatory functions, gene networks, and biological pathways involved in response of wheat root to a set of abiotic stresses. The meta-analysis using Fisher method (FDR<0.05) identified consensus 526 DEGs from 55,367 probe sets. Although the annotated expression data are limited for wheat, the functional analysis based on the data from model plants could identify the up-regulated seven regulatory genes involved in chromosome organization and response to oxygen-containing compounds. WGCNA identified four gene modules that were mostly associated with the ribosome biogenesis and polypeptide synthesis. This study's findings enhance our understanding of key players and gene networks related to wheat root response to multiple abiotic stresses.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran; Researcher of Sugar Beet Seed Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Morteza Derakhti-Dizaji
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Davod Dadashi
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Maryam Chalekaei
- Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Iran
| | - Ghader Rostami-Tobnag
- Department of Horticulture, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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13
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Xu L, Lan Y, Lin M, Zhou H, Ying S, Chen M. Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet ( Pennisetum glaucum). Int J Mol Sci 2024; 25:2470. [PMID: 38473718 DOI: 10.3390/ijms25052470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.
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Affiliation(s)
- Liang Xu
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Ying Lan
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Miaohong Lin
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Hongkai Zhou
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Sheng Ying
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Miao Chen
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
- Shenzhen Institute, Guangdong Ocean University, Shenzhen 518120, China
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Goyal E, Singh AK, Mahajan MM, Kanika K. Comparative transcriptome profiling of contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes under heat stress. Mol Biol Rep 2024; 51:283. [PMID: 38324135 DOI: 10.1007/s11033-024-09233-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: 08/15/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop's molecular responses to heat stress needs to be gained. METHODS AND RESULTS In the present study, a comparative RNA sequencing analysis was done in the leaf tissue of the finger millet, between the heat-sensitive (KJNS-46) and heat-tolerant (PES-110) cultivars of Ragi, in response to high temperatures. On average, each sample generated about 24 million reads. Interestingly, a comparison of transcriptomic profiling identified 684 transcripts which were significantly differentially expressed genes (DEGs) examined between the heat-stressed samples of both genotypes. The heat-induced change in the transcriptome was confirmed by qRT-PCR using a set of randomly selected genes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress specifically heat, oxidation-reduction process, water deprivation, and changes in heat shock protein (HSP) and transcription factors, calcium signaling, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes involved in housekeeping or related to basal regulatory processes. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., not yet characterized. CONCLUSION These findings highlight the importance of candidate genes, such as HSPs and pathways that can confer tolerance towards heat stress in ragi. These results will provide valuable information to improve the heat tolerance in heat-susceptible agronomically important varieties of ragi and other crops.
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Affiliation(s)
- Etika Goyal
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Amit Kumar Singh
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Mahesh Mohanrao Mahajan
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India
| | - Kumar Kanika
- Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India.
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15
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Jia M, Ni Y, Zhao H, Liu X, Yan W, Zhao X, Wang J, He B, Liu H. Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola. BMC PLANT BIOLOGY 2024; 24:64. [PMID: 38262910 PMCID: PMC10804834 DOI: 10.1186/s12870-024-04728-y] [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: 05/26/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Corynespora leaf spot is a common leaf disease occurring in sesame, and the disease causes leaf yellowing and even shedding, which affects the growth quality of sesame. At present, the mechanism of sesame resistance to this disease is still unclear. Understanding the resistance mechanism of sesame to Corynespora leaf spot is highly important for the control of infection. In this study, the leaves of the sesame resistant variety (R) and the sesame susceptible variety (S) were collected at 0-48 hpi for transcriptome sequencing, and used a combined third-generation long-read and next-generation short-read technology approach to identify some key genes and main pathways related to resistance. RESULTS The gene expression levels of the two sesame varieties were significantly different at 0, 6, 12, 24, 36 and 48 hpi, indicating that the up-regulation of differentially expressed genes in the R might enhanced the resistance. Moreover, combined with the phenotypic observations of sesame leaves inoculated at different time points, we found that 12 hpi was the key time point leading to the resistance difference between the two sesame varieties at the molecular level. The WGCNA identified two modules significantly associated with disease resistance, and screened out 10 key genes that were highly expressed in R but low expressed in S, which belonged to transcription factors (WRKY, AP2/ERF-ERF, and NAC types) and protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, and RLK-Pelle_WAK types). These genes could be the key response factors in the response of sesame to infection by Corynespora cassiicola. GO and KEGG enrichment analysis showed that specific modules could be enriched, which manifested as enrichment in biologically important pathways, such as plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione metabolism, MAPK and other stress-related pathways. CONCLUSIONS This study provides an important resource of genes contributing to disease resistance and will deepen our understanding of the regulation of disease resistance, paving the way for further molecular breeding of sesame.
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Affiliation(s)
- Min Jia
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Yunxia Ni
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
| | - Hui Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xintao Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Wenqing Yan
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xinbei Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Jing Wang
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Bipo He
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Hongyan Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
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Dhawi F. Utilizing In Silico Approaches to Investigate the Signaling Pathway's Crucial Function in Pennisetum glaucum Under Thermal Stress. Evol Bioinform Online 2023; 19:11769343231211072. [PMID: 38020532 PMCID: PMC10655657 DOI: 10.1177/11769343231211072] [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: 08/11/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Pearl millet (Pennisetum glaucum (L.)) is a remarkable cereal crop known for its ability to thrive in challenging environmental conditions. Despite its resilience, the intricate molecular mechanisms behind its toughness remain a mystery. To address this knowledge gap, we conducted advanced next-generation RNA sequencing. This approach allowed us to compare the gene expression profiles of pearl millet seedlings exposed to heat stress with those grown under standard conditions. Our main focus was on the shoots of 13-day-old pearl millet plants, which we subjected to a brief heat stress episode at 50°C for 60 seconds. Within the vast genomic landscape comprising 36 041 genes, we successfully identified a set of 10 genes that exhibited significant fold changes, ranging from 11 to 14-fold compared to the control conditions. These 10 genes were previously unknown to have such substantial changes in expression compared to the control. To uncover the functional significance hidden within these transcriptomic findings, we utilized computational tools such as MEME, String, and phylogenetic tree analysis. These efforts collectively revealed conserved domains within the transcriptomic landscape, hinting at potential functions associated with these genetic sequences. Of particular note, the distinct transcriptomic patterns specific to pearl millet leaves under thermal stress shed light on intricate connections to fundamental biological processes. These processes included the Ethylene-activated signaling pathway, Regulation of intracellular signal transduction, Negative regulation of signal transduction, Protein autophosphorylation, and Intracellular signal transduction. Together, these processes provide insight into the molecular strategies employed by pearl millet to overcome thermal stress challenges. By integrating cutting-edge RNA sequencing techniques and computational analyses, we have embarked on unraveling the genetic components and pathways that empower pearl millet's resilience in the face of adversity. This newfound understanding has the potential to not only advance our knowledge of plant stress responses but also contribute to enhancing crop resilience in challenging environmental conditions.
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Affiliation(s)
- Faten Dhawi
- Agricultural Biotechnology Department, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
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17
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Zhang P, Zhang F, Wu Z, Cahaeraduqin S, Liu W, Yan Y. Analysis on the salt tolerance of Nitraria sibirica Pall. based on Pacbio full-length transcriptome sequencing. PLANT CELL REPORTS 2023; 42:1665-1686. [PMID: 37479883 DOI: 10.1007/s00299-023-03052-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
KEY MESSAGE Nitraria sibirica Pall. regulates its tolerance to salt stress mainly by adjusting ion balance, modifying cell wall structure, and activating signal transduction pathways. N. sibirica, as a typical halophyte, can not only effectively restore saline-alkali land, but also has high economic value. However, studies on its salt tolerance at combining molecular and physiological levels were limited. In this study, the salt tolerance of N. sibirica was analyzed based on Pacbio full-length transcriptome sequencing, and the salt tolerance in the physiological level was verified by key genes. The results showed that 89,017 full-length transcripts were obtained, of which 84,632 sequences were annotated. A total of 86,482 coding sequences (CDS) were predicted and 6561 differentially expressed genes (DEGs) were identified. DEGs were significantly enriched in "sodium ion homeostasis", "response to osmotic stress", "reactive oxygen species metabolic process", "defense response by cell wall thickening", "signal transduction", etc. The expression levels for most of these DEGs increased under salt stress. A total of 69 key genes were screened based on weighted gene co-expression network analysis (WGCNA), of which 33 were first reported on salt tolerance. Moreover, NsRabE1c gene with the highest expression level was selected to verify its salt tolerance. Over-expression of NsRabE1c gene enhanced the germination potential and root length of transgenic Arabidopsis thaliana plants without salt treatment as compared to those of Col-0 and AtRabE1c mutant. The expression levels of NsRabE1c decreased in the growth stagnation phase, while significantly increased in the growth recovery phase under salt stress. We predicted that NsRabE1c gene help N. sibirica resist salt stress through the regulation of plant growth. The results of this study deepen the understanding of salinity resistance in N. sibirica.
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Affiliation(s)
- Panpan Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengxiang Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiheng Wu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Sunaer Cahaeraduqin
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Liu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yongqing Yan
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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18
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Li J, Zhang C, Mipam TD, Zhou Q, Chen S. Effects of Climatic Change on Phylogeography and Ecological Niche of the Endemic Herb Elymus breviaristatus on the Qinghai-Tibet Plateau. PLANTS (BASEL, SWITZERLAND) 2023; 12:3326. [PMID: 37765492 PMCID: PMC10535585 DOI: 10.3390/plants12183326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is crucial to understand the distribution and differentiation of genetic variation within species. Elymus breviaristatus, an ecologically important rare grass species with strong resistance, is restricted to a limited area of the QTP. In this study, we investigated the phylogeography of E. breviaristatus using five chloroplast genes and spacer regions in natural populations distributed along the eastern QTP. We identified a total of 25 haplotypes among 216 individuals from 18 E. breviaristatus populations, which were further classified into four haplogroups based on geographical distribution and haplotype network analysis. Notably, we did not observe any signs of population expansion. High genetic diversity was exhibited at both species and population levels, with precipitation being the main limiting factor for population genetic diversity levels. Higher genetic diversity was exhibited by populations located near the Mekong-Salween Divide genetic barrier, suggesting that they may have served as a glacial refuge. The significant pattern of genetic differentiation by environmental isolation highlights the influence of heterogeneous environments on the genetic structure of E. breviaristatus populations. Additionally, the results of ecological niche models indicated that the geographic distribution of E. breviaristatus populations has decreased rapidly since the Last Glacial Maximum but is not threatened by future global warming.
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Affiliation(s)
- Jin Li
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | | | - Tserang Donko Mipam
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Shiyong Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
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Jin Y, Luo J, Yang Y, Jia J, Sun M, Wang X, Khan I, Huang D, Huang L. The evolution and expansion of RWP-RK gene family improve the heat adaptability of elephant grass (Pennisetum purpureum Schum.). BMC Genomics 2023; 24:510. [PMID: 37653366 PMCID: PMC10472707 DOI: 10.1186/s12864-023-09550-8] [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: 01/28/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Along with global warming, resulting in crop production, exacerbating the global food crisis. Therefore, it is urgent to study the mechanism of plant heat resistance. However, crop resistance genes were lost due to long-term artificial domestication. By analyzing the potential heat tolerance genes and molecular mechanisms in other wild materials, more genetic resources can be provided for improving the heat tolerance of crops. Elephant grass (Pennisetum purpureum Schum.) has strong adaptability to heat stress and contains abundant heat-resistant gene resources. RESULTS Through sequence structure analysis, a total of 36 RWP-RK members were identified in elephant grass. Functional analysis revealed their close association with heat stress. Four randomly selected RKDs (RKD1.1, RKD4.3, RKD6.6, and RKD8.1) were analyzed for expression, and the results showed upregulation under high temperature conditions, suggesting their active role in response to heat stress. The members of RWP-RK gene family (36 genes) in elephant grass were 2.4 times higher than that of related tropical crops, rice (15 genes) and sorghum (15 genes). The 36 RWPs of elephant grass contain 15 NLPs and 21 RKDs, and 73% of RWPs are related to WGD. Among them, combined with the DAP-seq results, it was found that RWP-RK gene family expansion could improve the heat adaptability of elephant grass by enhancing nitrogen use efficiency and peroxidase gene expression. CONCLUSIONS RWP-RK gene family expansion in elephant grass is closely related to thermal adaptation evolution and speciation. The RKD subgroup showed a higher responsiveness than the NLP subgroup when exposed to high temperature stress. The promoter region of the RKD subgroup contains a significant number of MeJA and ABA responsive elements, which may contribute to their positive response to heat stress. These results provided a scientific basis for analyzing the heat adaptation mechanism of elephant grass and improving the heat tolerance of other crops.
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Affiliation(s)
- Yarong Jin
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Sun
- 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
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Dejun Huang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Zhang J, Wang D, Chen P, Zhang C, Yao S, Hao Q, Agassin RH, Ji K. The Transcriptomic Analysis of the Response of Pinus massoniana to Drought Stress and a Functional Study on the ERF1 Transcription Factor. Int J Mol Sci 2023; 24:11103. [PMID: 37446285 DOI: 10.3390/ijms241311103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Pinus massoniana is a major fast-growing timber tree species planted in arid areas of south China, which has a certain drought-resistant ability. However, severe drought and long-term water shortage limit its normal growth and development. Therefore, in this study, physiological indices, and the transcriptome sequencing and cloning of AP2/ERF transcription factor of P. massonsiana were determined to clarify its molecular mechanism of drought stress. The results showed that stomatal conductance (Gs) content was significantly decreased, and superoxide dismutase (SOD) activity, and malondialdehyde (MDA) and abscisic acid (ABA) content were significantly increased under drought stress. Transcriptomic analysis revealed that compared to the control, 9, 3550, and 4142 unigenes with differential expression were identified by comparing plants subjected to light, moderate or severe drought. AP2/ERF with high expression was screened out for cloning. To investigate the biological functions of ERF1, it was over-expressed in wild-type Populus davdianaand × P. bolleana via the leaf disc method. Under drought stress, compared to wild-type plants, ERF1 over-expressing poplar lines (OE) maintained a higher photosynthetic rate and growth, while the transpiration rate and stomatal conductance significantly decreased and water use efficiency was improved, indicating that drought tolerance was enhanced. This study provides an insight into the molecular mechanism of drought stress adaptation in P. massoniana.
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Affiliation(s)
- Jinfeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Peizhen Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qingqing Hao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Romaric Hippolyte Agassin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Krzyżak J, Rusinowski S, Sitko K, Szada-Borzyszkowska A, Stec R, Janota P, Jensen E, Kiesel A, Pogrzeba M. The effect of combined drought and trace metal elements stress on the physiological response of three Miscanthus hybrids. Sci Rep 2023; 13:10452. [PMID: 37380788 DOI: 10.1038/s41598-023-37564-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/23/2023] [Indexed: 06/30/2023] Open
Abstract
Drought is a serious threat worldwide and has a significant impact on agricultural production and soil health. It can pose an even greater threat when it involves land contaminated with trace metal element (TMEs). To prevent desertification, such land should be properly managed and growing Miscanthus for energy or raw material purposes could be a solution. The effects of drought and TMEs were studied in a pot experiment on three different Miscanthus hybrids (conventional Miscanthus × giganteus, TV1 and GNT10) considering growth parameters, photosynthetic parameters and elemental composition of roots, rhizomes and shoots. GNT10 was characterised by the weakest gas exchange among the hybrids, which was compensated by the highest number of leaves and biomass. The strongest correlations between the studied parameters were found for TV1, which might indicate a high sensitivity to TME stress. For M × g and GNT10, the main mechanisms for coping with stress seem to be biomass management through number of shoots and leaves and gas exchange. The main factor determining the extent of accumulation of TMEs was the amount of water applied in the experimental treatment, which was related to the location of the plant in the aniso-isohydric continuum. GNT10 was the most resistant plant to combined stress, while it responded similarly to TV1 when drought and trace metal elements were applied separately.
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Affiliation(s)
- Jacek Krzyżak
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland
| | - Szymon Rusinowski
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland
| | - Krzysztof Sitko
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland
- Plant Ecophysiology Team, University of Silesia in Katowice, 28 Jagiellońska Street, 40-032, Katowice, Poland
| | | | - Radosław Stec
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland
| | - Paulina Janota
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland
| | - Elaine Jensen
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - Andreas Kiesel
- Biobased Resources in the Bioeconomy (340B), Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Marta Pogrzeba
- Institute for Ecology of Industrial Areas, 6 Kossutha Street, 40-844, Katowice, Poland.
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22
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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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Lv J, Xu Y, Dan X, Yang Y, Mao C, Ma X, Zhu J, Sun M, Jin Y, Huang L. Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses. Genetica 2023:10.1007/s10709-023-00188-8. [PMID: 37266766 DOI: 10.1007/s10709-023-00188-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
In addition to their roles in developmental and metabolic processes, MYB transcription factors play crucial roles in plant defense mechanisms and stress responses. A comprehensive analysis of six pearl millet genomes revealed the presence of 1133 MYB genes, which can be classified into four phylogenetically distinct subgroups. The duplication pattern of MYB genes across the pearl millet genomes demonstrates their conserved and similar evolutionary history. Overall, MYB genes were observed to be involved in drought and heat stress responses, with stronger differential expressed observed in root tissues. Multiple analyses indicated that MYB genes mediate abiotic stress responses by modulating abscisic acid-related pathways, circadian rhythms, and histone modification processes. A substantial number of duplicated genes were determined to exhibit differential expression under abiotic stress. The consistent positive expression trend observed in duplicated gene pairs, such as PMA5G04432.1 and PMA2G00728.1, across various abiotic stresses suggests that duplicated MYB genes plays a key role in the evolution of adaptive responses of pearl millet to abiotic stresses.
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Affiliation(s)
- Jinhang Lv
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Yue Xu
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Xuming Dan
- Department of The College of Life Sciences, Sichuan University, Sichuan, China
| | - Yuchen Yang
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Chunli Mao
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Xixi Ma
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Jie Zhu
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Min Sun
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Yarong Jin
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China.
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Huang B, Yan H, Sun M, Jin Y. Novel discovery in roles of structural variations and RWP-RK transcription factors in heat tolerance for pearl millet. STRESS BIOLOGY 2023; 3:12. [PMID: 37676357 PMCID: PMC10442032 DOI: 10.1007/s44154-023-00092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/03/2023] [Indexed: 09/08/2023]
Abstract
Global warming adversely affects crop production worldwide. Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants. However, the roles of structural variations (SVs) in heat stress tolerance remain unclear. In a recent article, Yan et al. (Nat Genet 1-12, 2023) constructed the first pan-genome of pearl millet (Pennisetum glaucum) and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates. Through multi-omics analyses integrating by pan-genomics, comparative genomics, transcriptomics, population genetics and and molecular biological technologies, they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet. The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.
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Affiliation(s)
- Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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25
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Samarina L, Wang S, Malyukova L, Bobrovskikh A, Doroshkov A, Koninskaya N, Shkhalakhova R, Matskiv A, Fedorina J, Fizikova A, Manakhova K, Loshkaryova S, Tutberidze T, Ryndin A, Khlestkina E. Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( Camellia sinensis (L.) Kuntze). FRONTIERS IN PLANT SCIENCE 2023; 14:1145793. [PMID: 37235017 PMCID: PMC10206121 DOI: 10.3389/fpls.2023.1145793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Songbo Wang
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandr Bobrovskikh
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Doroshkov
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Jaroslava Fedorina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Anastasia Fizikova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Karina Manakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Svetlana Loshkaryova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Tsiala Tutberidze
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Elena Khlestkina
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg, Russia
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Awan SA, Khan I, Rizwan M, Irshad MA, Xiaosan W, Zhang X, Huang L. Reduction in the cadmium (Cd) accumulation and toxicity in pearl millet (Pennisetum glaucum L.) by regulating physio-biochemical and antioxidant defense system via soil and foliar application of melatonin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 328:121658. [PMID: 37075919 DOI: 10.1016/j.envpol.2023.121658] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/12/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
Cadmium (Cd) is among the toxic pollutants that harms the both animals and plants. The natural antioxidant, melatonin can improve Cd-stress tolerance but its potential role in reducing Cd stress and resilience mechanisms in pearl millet (Pennisetum glaucum L.) is remain unclear. The present study suggests that Cd causes severe oxidative damage by decreasing photosynthesis, and increasing reactive oxygen species (ROS), malondialdehyde content (MDA), and Cd content in different parts of pearl millet. However, exogenous melatonin (soil application and foliar treatment) mitigated the Cd toxicity and enhanced the growth, antioxidant defense system, and differentially regulated the expression of antioxidant-responsive genes i. e superoxide dismutase SOD-[Fe] 2, Fe-superoxide dismutase, Peroxiredoxin 2C, and L-ascorbate peroxidase-6. The results showed that foliar melatonin at F-200/50 significantly increased the plant height, chlorophyll a, b, a+b and carotenoids by 128%, 121%, 150%, 122%, and 69% over the Cd treatment, respectively. The soil and foliar melatonin at S-100/50 and F-100/50 reduced the ROS by 36%, and 44%, and MDA by 42% and 51% over the Cd treatment, respectively. Moreover, F200/50 significantly boosted the activities of antioxidant enzymes i. e SOD by 141%, CAT 298%, POD 117%, and APX 155% over the Cd treatment. Similarly, a significant reduction in Cd content in root, stem, and leaf was found on exposure to higher concentrations of exogenous melatonin. These findings suggest that exogenous melatonin may significantly and differentially improve the tolerance to Cd stress in crop plants. However, field applications, type of plant species, concentration of dose, and type of stress may vary with the degree of tolerance in crop plants.
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Affiliation(s)
- Samrah Afzal Awan
- College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Imran Khan
- College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Atif Irshad
- Department of Environmental Sciences, The University of Lahore, Lahore, Pakistan
| | - Wang Xiaosan
- College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Mi X, Yang C, Qiao D, Tang M, Guo Y, Liang S, Li Y, Chen Z, Chen J. De novo full length transcriptome analysis of a naturally caffeine-free tea plant reveals specificity in secondary metabolic regulation. Sci Rep 2023; 13:6015. [PMID: 37045909 PMCID: PMC10097665 DOI: 10.1038/s41598-023-32435-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Tea plants are crops with economic, health and cultural value. Catechin, caffeine and theanine are the main secondary metabolites of taste. In the process of germplasm collection, we found a resource in the Sandu Aquatic Autonomous County of Guizhou (SDT) that possessed significantly different characteristic metabolites compared with the cultivar 'Qiancha 1'. SDT is rich in theobromine and theophylline, possesses low levels of (-)-epicatechin-3-gallate, (-)-epigallocatechin-3-gallate, and theanine content, and is almost free of caffeine. However, research on this tea resource is limited. Full-length transcriptome analysis was performed to investigate the transcriptome and gene expression of these metabolites. In total, 78,809 unique transcripts were obtained, of which 65,263 were complete coding sequences. RNA-seq revealed 3415 differentially expressed transcripts in the tender leaves of 'Qiancha 1' and 'SDT'. Furthermore, 2665, 6231, and 2687 differentially expressed transcripts were found in different SDT tissues. These differentially expressed transcripts were enriched in flavonoid and amino acid metabolism processes. Co-expression network analysis identified five modules associated with metabolites and found that genes of caffeine synthase (TCS) may be responsible for the low caffeine content in SDT. Phenylalanine ammonia lyase (PAL), glutamine synthetase (GS), glutamate synthase (GOGAT), and arginine decarboxylase (ADC) play important roles in the synthesis of catechin and theanine. In addition, we identified that ethylene resposive factor (ERF) and WRKY transcription factors may be involved in theanine biosynthesis. Overall, our study provides candidate genes to improve understanding of the synthesis mechanisms of these metabolites and provides a basis for molecular breeding of tea plant.
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Affiliation(s)
- Xiaozeng Mi
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Chun Yang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Dahe Qiao
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Mengsha Tang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Yan Guo
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Sihui Liang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Yan Li
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Zhengwu Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China
| | - Juan Chen
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, 1 Jin'nong Road, Guiyang, 550006, Guizhou, China.
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Atamian HS, Funk JL. Physiological and transcriptomic responses of two Artemisia californica populations to drought: implications for restoring drought-resilient native communities. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
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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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30
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Shekhar S, Prasad AS, Banjare K, Kaushik A, Mannade AK, Dubey M, Patil A, Premi V, Vishwakarma AK, Sao A, Saxena RR, Dubey A, Chandel G. LMT db: A comprehensive transcriptome database for climate-resilient, nutritionally rich little millet ( Panicum sumatrense). FRONTIERS IN PLANT SCIENCE 2023; 14:1106104. [PMID: 36993866 PMCID: PMC10041709 DOI: 10.3389/fpls.2023.1106104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
Little millet (Panicum sumatrense) a native of Chhattisgarh, belongs to the minor millet group and is primarily known as a climate-resilient and nutritionally rich crop. However, due to the lack of enough Omic studies on the crop, the scientific community has largely remained unaware of the potential of this crop, resulting in less scope for its utilization in crop improvement programs. Looking at global warming, erratic climate change, nutritional security, and limited genetic information available, the Little Millet Transcriptome Database (LMTdb) (https://igkv.ac.in/xenom/index.aspx) was conceptualized upon completion of the transcriptome sequencing of little millet with the aim of deciphering the genetic signatures of this largely unknown crop. The database was developed with the view of providing information about the most comprehensive part of the genome, the 'Transcriptome'. The database includes transcriptome sequence information, functional annotation, microsatellite markers, DEGs, and pathway information. The database is a freely available resource that provides breeders and scientists a portal to search, browse, and query data to facilitate functional and applied Omic studies in millet crops.
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Affiliation(s)
- Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Archana S. Prasad
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Kalpana Banjare
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Abhijeet Kaushik
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Ajit K. Mannade
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Mahima Dubey
- Department of Vegetable Biotechnology, VNR Seeds Private Limited, Raipur, India
| | - Arun Patil
- Department of Vegetable Biotechnology, VNR Seeds Private Limited, Raipur, India
| | - Vinay Premi
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | | | - Abhinav Sao
- Department of Genetics and Plant Breeding, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Ravi R. Saxena
- Knowledge and Technology Resource Centre, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Amit Dubey
- Chhattisgarh Council of Science and Technology, Raipur, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
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Yan H, Sun M, Zhang Z, Jin Y, Zhang A, Lin C, Wu B, He M, Xu B, Wang J, Qin P, Mendieta JP, Nie G, Wang J, Jones CS, Feng G, Srivastava RK, Zhang X, Bombarely A, Luo D, Jin L, Peng Y, Wang X, Ji Y, Tian S, Huang L. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 2023; 55:507-518. [PMID: 36864101 PMCID: PMC10011142 DOI: 10.1038/s41588-023-01302-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/18/2023] [Indexed: 03/04/2023]
Abstract
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.
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Affiliation(s)
- Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | | | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- Key Laboratory of Bio-Source and Environmental Conservation, School of Life Science, Sichuan University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | | | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Aureliano Bombarely
- Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC, Valencia, Spain
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China.
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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32
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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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Khan I, Awan SA, Rizwan M, Akram MA, Zia-Ur-Rehman M, Wang X, Zhang X, Huang L. Physiological and transcriptome analyses demonstrate the silver nanoparticles mediated alleviation of salt stress in pearl millet (Pennisetum glaucum L). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120863. [PMID: 36526056 DOI: 10.1016/j.envpol.2022.120863] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Pearl millet (Pennisetum glaucum L.) is a highly nutritive-value summer-annual forage crop used for hay, silage, grazing, and green chop. However, abiotic stresses including salinity negatively affect its growth and productivity. Furthermore, the nanotechnology is attaining greater consideration to reduce the impact of environmental stresses in plants. In the present study, transcriptome responses of silver nanoparticles (AgNPs) in pearl millet under salinity were investigated. The treatments were given as Control, NaCl (250 mM), AgNPs (20 mg/L), and NaCl + AgNPs to pearl millet seedlings after thirteen days of seed sowing. After 1 h of given treatments, leaf samples were collected and subjected to physio-chemical examination and transcriptome analyses. Salt stress increased the hydrogen peroxide (H2O2), malondialdehyde (MDA) content, and proline as compared to other treatments. In addition, the combined applications of NaCl + AgNPs ameliorated the oxidative damage by increasing antioxidant enzymes activities including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). Furthermore, RNA sequencing data showed 6016 commonly annotated Differentially Expressed Transcripts (DETs) among various treated combinations. Among them, 427 transcripts were upregulated, and 136 transcripts were downregulated at nanoparticles vs control, 1469 upregulated and 1182 downregulated at salt vs control, 494 upregulated and 231 downregulated at salt + nanoparticles vs control, 783 upregulated and 523 downregulated at nanoparticles vs salt. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that Mitogen-activated protein kinase (MAPK) signaling pathway, biosynthesis of secondary metabolites, and plant hormonal signal transduction pathway were the enriched among all identified pathways. In addition, Reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) showed that salinity up regulated the relative expression of DETs in pearl millet while, AgNPs optimized their expression that are associated with various molecular and metabolic functions. Overall, AgNPs treatments effectively improved the morphology, physiology, biochemistry, and gene expression pattern under salinity which could be attributed to positive impacts of AgNPs on pearl millet.
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Affiliation(s)
- Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Samrah Afzal Awan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China; College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Muhammad Zia-Ur-Rehman
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Xiaosan Wang
- 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
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Chanwala J, Khadanga B, Jha DK, Sandeep IS, Dey N. MYB Transcription Factor Family in Pearl Millet: Genome-Wide Identification, Evolutionary Progression and Expression Analysis under Abiotic Stress and Phytohormone Treatments. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020355. [PMID: 36679070 PMCID: PMC9865524 DOI: 10.3390/plants12020355] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 11/06/2022] [Indexed: 06/03/2023]
Abstract
Transcription factors (TFs) are the regulatory proteins that act as molecular switches in controlling stress-responsive gene expression. Among them, the MYB transcription factor family is one of the largest TF family in plants, playing a significant role in plant growth, development, phytohormone signaling and stress-responsive processes. Pearl millet (Pennisetum glaucum L.) is one of the most important C4 crop plants of the arid and semi-arid regions of Africa and Southeast Asia for sustaining food and fodder production. To explore the evolutionary mechanism and functional diversity of the MYB family in pearl millet, we conducted a comprehensive genome-wide survey and identified 279 MYB TFs (PgMYB) in pearl millet, distributed unevenly across seven chromosomes of pearl millet. A phylogenetic analysis of the identified PgMYBs classified them into 18 subgroups, and members of the same group showed a similar gene structure and conserved motif/s pattern. Further, duplication events were identified in pearl millet that indicated towards evolutionary progression and expansion of the MYB family. Transcriptome data and relative expression analysis by qRT-PCR identified differentially expressed candidate PgMYBs (PgMYB2, PgMYB9, PgMYB88 and PgMYB151) under dehydration, salinity, heat stress and phytohormone (ABA, SA and MeJA) treatment. Taken together, this study provides valuable information for a prospective functional characterization of the MYB family members of pearl millet and their application in the genetic improvement of crop plants.
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Affiliation(s)
- Jeky Chanwala
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Badrinath Khadanga
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar 751023, India
| | - Deepak Kumar Jha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Inavolu Sriram Sandeep
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar 751023, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar 751023, India
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Qu M, Zheng Y, Bi L, Yang X, Shang P, Zhou X, Zeng B, Shen B, Li W, Fan Y, Zeng B. Comparative transcriptomic analysis of the gene expression and underlying molecular mechanism of submergence stress response in orchardgrass roots. FRONTIERS IN PLANT SCIENCE 2023; 13:1104755. [PMID: 36704155 PMCID: PMC9871833 DOI: 10.3389/fpls.2022.1104755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Submergence stress creates a hypoxic environment. Roots are the first plant organ to face these low-oxygen conditions, which causes damage and affects the plant growth and yield. Orchardgrass (Dactylis glomerata L.) is one of the most important cold-season forage grasses globally. However, their submergence stress-induced gene expression and the underlying molecular mechanisms of orchardgrass roots are still unknown. METHODS Using the submergence-tolerant 'Dianbei' and submergence-sensitive 'Anba', the transcriptomic analysis of orchardgrass roots at different time points of submergence stress (0 h, 8 h, and 24 h) was performed. RESULTS We obtained 118.82Gb clean data by RNA-Seq. As compared with the control, a total of 6663 and 9857 differentially expressed genes (DEGs) were detected in Dianbei, while 7894 and 11215 DEGs were detected in Anba at 8 h and 24 h post-submergence-stress, respectively. Gene Ontology (GO) enrichment analysis obtained 986 terms, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis obtained 123 pathways. Among them, the DEGs in plant hormones, mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction were significantly differentially expressed in Dianbei, but not in Anba. DISCUSSION This study was the first to molecularly elucidate the submergence stress tolerance in the roots of two orchardgrass cultivars. These findings not only enhanced our understanding of the orchardgrass submergence tolerance, but also provided a theoretical basis 36 for the cultivation of submergence-tolerant forage varieties.
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Affiliation(s)
- Minghao Qu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yuqian Zheng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Lei Bi
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xingyun Yang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Panpan Shang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiaoli Zhou
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Bingna Shen
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wenwen Li
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Fan
- Institute of Prataculture, Chongqing Academy of Animal Science, Chongqing, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing University Herbivore Engineering Research Center, Chongqing, China
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36
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Yang Z, Nie G, Feng G, Xu X, Li D, Wang X, Huang L, Zhang X. Genome-wide identification of MADS-box gene family in orchardgrass and the positive role of DgMADS114 and DgMADS115 under different abiotic stress. Int J Biol Macromol 2022; 223:129-142. [PMID: 36356860 DOI: 10.1016/j.ijbiomac.2022.11.027] [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: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Abiotic stress, a major factor limit growth and productivity of major crops. Orchardgrass is one of the most important cool-season forage grasses in the world, and it is highly tolerant to abiotic stress. The MADS-box transcription factor family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, MADS-box transcription factors in orchardgrass, especially those involved in abiotic stress, have not yet been elucidated. Here, 123 DgMADS-box members were identified in orchardgrass and a detailed overview has been presented. Syntenic analysis indicated that the expansion of the DgMADS-box genes in orchardgrass is mainly dependent on tandem duplication events. Some DgMADS-box genes were induced by multiple abiotic stresses, indicating that these genes may play critical regulatory roles in orchardgrass response to various abiotic stresses. Heterologous expression showed that DgMADS114 and DgMADS115 could enhance stress tolerance of transgenic Arabidopsis, as revealed by longer root length or higher survival rates under PEG, NaCl, ABA, and heat stress. The results of this study provide a scientific basis for clarifying the functional characterization of MADS-box genes in orchardgrass in response to environmental stress can be further used to improve forages and crops via breeding programs.
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Affiliation(s)
- Zhongfu Yang
- 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
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xia Wang
- 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.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Comprehensive Analysis of Transcriptome and Metabolome Elucidates the Molecular Regulatory Mechanism of Salt Resistance in Roots of Achnatherum inebrians Mediated by Epichloë gansuensis. J Fungi (Basel) 2022; 8:jof8101092. [PMID: 36294657 PMCID: PMC9605608 DOI: 10.3390/jof8101092] [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: 07/07/2022] [Revised: 09/15/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Salinization of soil is a major environmental risk factor to plant functions, leading to a reduction of productivity of crops and forage. Epichloë gansuensis, seed-borne endophytic fungi, establishes a mutualistic symbiotic relationship with Achnatherum inebrians and confers salt tolerance in the host plants. In this study, analysis of transcriptome and metabolome was used to explore the potential molecular mechanism underlying the salt-adaptation of A. inebrians roots mediated by E. gansuensis. We found that E. gansuensis played an important role in the gene expression of the host’s roots and regulated multiple pathways involved in amino acid metabolism, carbohydrate metabolism, TCA cycle, secondary metabolism, and lipid metabolism in the roots of A. inebrians. Importantly, E. gansuensis significantly induced the biological processes, including exocytosis, glycolytic process, fructose metabolic process, and potassium ion transport in roots of host plants at transcriptional levels, and altered the pathways, including inositol phosphate metabolism, galactose metabolism, starch, and sucrose metabolism at metabolite levels under NaCl stress. These findings provided insight into the molecular mechanism of salt resistance in roots of A. inebrians mediated by E. gansuensis and could drive progress in the cultivation of new salt-resistance breeds with endophytes.
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Samtiya M, Aluko RE, Dhaka N, Dhewa T, Puniya AK. Nutritional and health-promoting attributes of millet: current and future perspectives. Nutr Rev 2022; 81:684-704. [PMID: 36219789 DOI: 10.1093/nutrit/nuac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Millet is consumed as a staple food, particularly in developing countries, is part of the traditional diet in a number of relatively affluent countries, and is gaining popularity throughout the world. It is a valuable dietary energy source. In addition to high caloric value, several health-promoting attributes have been reported for millet seeds. This review describes many nutritional characteristics of millet seeds and their derivatives that are important to human health: antioxidant, antihypertensive, immunomodulatory or anti-inflammatory, antibacterial or antimicrobial, hypocholesterolemic, hypoglycemic, and anti-carcinogenic potential, and their role as modulators of gut health. There are several varieties, but the main focus of this review is on pearl millet (Cenchrus americanus [synonym Pennisetum glaucum]), one of the most widely eaten millet crops grown in India, though other millet types are also covered. In this article, the health-promoting properties of the natural components (ie, proteins, peptides, polyphenols, polysaccharides, oil, isoflavones, etc.) present in millet seeds are discussed. Although many of these health benefits have been demonstrated using animal models in vitro studies, human intervention-feeding trials are required to confirm several of the potential health benefits of millet seeds. Based on the nutritional and health-promoting attributes known for pearl millet (discussed in this review), finger millet and foxtail millet are suggested as good candidates for use in future nutritional interventions for improved human health.
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Affiliation(s)
- Mrinal Samtiya
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Tejpal Dhewa
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Anil Kumar Puniya
- is with the Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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Babele PK, Kudapa H, Singh Y, Varshney RK, Kumar A. Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health. FRONTIERS IN PLANT SCIENCE 2022; 13:902536. [PMID: 36035707 PMCID: PMC9412166 DOI: 10.3389/fpls.2022.902536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/18/2022] [Indexed: 05/29/2023]
Abstract
The ever-changing climate and the current COVID-19 pandemic compound the problems and seriously impact agriculture production, resulting in socio-economic insecurities and imposing health implications globally. Most of the poor and malnourished population in the developing countries depends on agriculture for food, income, and employment. Impact of climate change together with the COVID-19 outbreak revealed immense problems highlighting the importance of mainstreaming climate-resilient and low input crops with more contemporary agriculture practices. Orphan millets play a vital role in the poor and malnourished population's livelihood, food and nutrition security. Recognizing their unique potential, the United Nations-Food and Agriculture Organization has announced the year 2023 as the "International Year of Millets". However, despite the unique properties for present and future agriculture of orphan millets, their cultivation is declining in many countries. As a result, millets have gained attention from researchers which eventually decelerated "multi-omics" resource generation. This review summarizes the benefits of millets and major barriers/ bottlenecks in their improvement. We also discuss the pre- and post-harvest technologies; policies required to introduce and establish millets in mainstream agriculture. To improve and ensure the livelihood of the poor/malnourished population, intensive efforts are urgently needed in advancing the research and development, implementing pre- and post-harvest technological intervention strategies, and making favorable policies for orphan crops to accomplish food and nutrition security. National and international collaborations are also indispensable to address the uncertain effects of climate change and COVID-19.
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Affiliation(s)
- Piyoosh K. Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yogeshwar Singh
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Murdoch's Centre for Crop Research & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Anil Kumar
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
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Shanker AK, Amirineni S, Bhanu D, Yadav SK, Jyothilakshmi N, Vanaja M, Singh J, Sarkar B, Maheswari M, Singh VK. High-resolution dissection of photosystem II electron transport reveals differential response to water deficit and heat stress in isolation and combination in pearl millet [ Pennisetum glaucum (L.) R. Br.]. FRONTIERS IN PLANT SCIENCE 2022; 13:892676. [PMID: 36035679 PMCID: PMC9412916 DOI: 10.3389/fpls.2022.892676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Heat and Water Deficit Stress (WDS) tend to impede and restrict the efficiency of photosynthesis, chlorophyll fluorescence, and maximum photochemical quantum yield in plants based on their characteristic ability to interfere with the electron transport system in photosystem II. Dissection of the electron transport pathway in Photosystem II (PSII) under water deficit and Heat Stress (HS) can be insightful in gaining knowledge on the various attributes of the photosynthetic performance of a plant. We attempt a high-resolution dissection of electron transport in PSII with studies on chlorophyll a fast fluorescence kinetics and non-photochemical quenching (NPQ) as a response to and recovery from these stresses in pearl millet [Pennisetum glaucum (L.) R. Br.] in isolation and combination. In this study, we bring out the mechanisms by which both heat and water stress, in isolation and in combination, affect the photosynthetic electron transport in Photosystem II. Our results indicate that oxygen evolution complex (OEC) damage is the primary effect of heat stress and is not seen with the same intensity in the water-stressed plants. Low exciton absorption flux in heat stress and combined stress was seen due to OEC damage, and this caused an electron transport traffic jam in the donor side of PS II. Both the specific energy flux model and the phenomenological flux model developed from the derived values in our study show that water deficit stress in combination with heat stress has a much stronger effect than the stresses in isolation on the overall electron transport pathway of the PS II in pearl millet plants.
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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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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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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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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Zhang X, Liu N, Lu H, Zhu L. Molecular Mechanism of Organic Pollutant-Induced Reduction of Carbon Fixation and Biomass Yield in Oryza sativa L. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4162-4172. [PMID: 35324172 DOI: 10.1021/acs.est.1c07835] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photosynthetic carbon fixation is fundamental for plant growth and is a key process driving the global carbon cycle. This study explored the mechanism of disturbed carbon fixation in Oryza sativa L. by organic pollutants 2,3,4,5-tetrachlorobiphenyl (CB 61), 4'-hydroxy-2,3,4,5-tetrachlorobiphenyl (4'-OH-CB 61), 2,2',4,4'-tetrabromo diphenyl ether (BDE 47), tricyclazole (TRI), and pyrene. The biomass of rice exposed to 4'-OH-CB 61, TRI, and BDE 47 was on average 80.63% of that of the control (p < 0.05), and the inhibition of net photosynthetic rate was 59.15% by 4'-OH-CB 61. Proteomics confirmed that 4'-OH-CB 61 significantly downregulated the enzymes in the photosynthetic carbon fixation pathway, which was attributed to the decrease in ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the rate-limiting enzyme in the Calvin cycle. In detail, decreased Rubisco activity (6.96-33.44%) and downregulated OsRBCS2-5 encoding small Rubisco subunits (-6.80 < log2FC < -2.13) by 4'-OH-CB 61, TRI, and BDE 47 were in line with biomass yield reduction. Molecular docking and dynamic simulation suggested that the three pollutants potentially competed with CO2 for binding to the active sites in Rubisco, leading to reduced CO2 capture efficiency. These results revealed the molecular mechanism of organic pollution-induced rice yield reduction, contributing to improving the understanding of crop growth and carbon sequestration capacity of organics-contaminated soils globally.
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Affiliation(s)
- Xinru Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Na Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
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Bhardwaj A, Devi P, Chaudhary S, Rani A, Jha UC, Kumar S, Bindumadhava H, Prasad PVV, Sharma KD, Siddique KHM, Nayyar H. 'Omics' approaches in developing combined drought and heat tolerance in food crops. PLANT CELL REPORTS 2022; 41:699-739. [PMID: 34223931 DOI: 10.1007/s00299-021-02742-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Global climate change will significantly increase the intensity and frequency of hot, dry days. The simultaneous occurrence of drought and heat stress is also likely to increase, influencing various agronomic characteristics, such as biomass and other growth traits, phenology, and yield-contributing traits, of various crops. At the same time, vital physiological traits will be seriously disrupted, including leaf water content, canopy temperature depression, membrane stability, photosynthesis, and related attributes such as chlorophyll content, stomatal conductance, and chlorophyll fluorescence. Several metabolic processes contributing to general growth and development will be restricted, along with the production of reactive oxygen species (ROS) that negatively affect cellular homeostasis. Plants have adaptive defense strategies, such as ROS-scavenging mechanisms, osmolyte production, secondary metabolite modulation, and different phytohormones, which can help distinguish tolerant crop genotypes. Understanding plant responses to combined drought/heat stress at various organizational levels is vital for developing stress-resilient crops. Elucidating the genomic, proteomic, and metabolic responses of various crops, particularly tolerant genotypes, to identify tolerance mechanisms will markedly enhance the continuing efforts to introduce combined drought/heat stress tolerance. Besides agronomic management, genetic engineering and molecular breeding approaches have great potential in this direction.
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Affiliation(s)
| | - Poonam Devi
- Department of Botany, Panjab University, Chandigarh, India
| | | | - Anju Rani
- Department of Botany, Panjab University, Chandigarh, India
| | | | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - H Bindumadhava
- Dr. Marri Channa Reddy Foundation (MCRF), Hyderabad, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India.
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Ajeesh Krishna TP, Maharajan T, Ceasar SA. Improvement of millets in the post-genomic era. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:669-685. [PMID: 35465206 PMCID: PMC8986959 DOI: 10.1007/s12298-022-01158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 05/16/2023]
Abstract
Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.
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Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
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Cheng L, Han S, Jiang J, Li H, Peng L. Transcriptome Analysis for Identification of Genes Related to Growth and Development, Digestion and Detoxification, Olfaction in the Litchi Stink Bug Tessaratoma papillosa. Front Physiol 2022; 12:774218. [PMID: 35140626 PMCID: PMC8818959 DOI: 10.3389/fphys.2021.774218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Tessaratoma papillosa is a major pest of Litchi chinensis and Dimocarpus longan. Adult and nymph secretions are not only harmful to plants but also to humans. At present, there are not a lot of research on T. papillosa, especially omics research. We used high-throughput sequencing technology to sequence the T. papillosa transcriptome and obtained 67,597 unigenes homologous to Halyomorpha halys (88.03%). Subsequently, RNA-SEQ and comparative analyses were performed on the 14 different developmental stages and tissues. A total of 462 unigenes related to growth and development, 1,851 unigenes related to digestion and detoxification, and 70 unigenes related to olfaction were obtained. Moreover, expression analysis showed that the T. papillosa major life activities genes are uniformly expressed across all developmental states. However, the adult midgut gene expression patterns were utterly different from that of the nymphs. Similarly, female fat body genes exhibited distinct expression patterns compared to that of males and nymphs. Thus, different developmental stages and physiological functions affect gene expression patterns. We also found that most of the differential genes were associated with cellular maintenance. This study will help understand the growth and development of litchi stink bugs, their choice of host plants, food digestion and detoxification, and their reproductive behavior. In addition, this result can provide reference information for some target genes in the process of control of T. papillosa.
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Affiliation(s)
- Lin Cheng
- Biological Control Research Institute, Fujian Agriculture and Forestry University, China Fruit Fly Research and Control Center of FAO/IAEA, Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
| | - Shuncai Han
- Biological Control Research Institute, Fujian Agriculture and Forestry University, China Fruit Fly Research and Control Center of FAO/IAEA, Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
| | - Jingtao Jiang
- Biological Control Research Institute, Fujian Agriculture and Forestry University, China Fruit Fly Research and Control Center of FAO/IAEA, Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
| | - Haichao Li
- Chinese Academy of Sciences Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Haichao Li,
| | - Lingfei Peng
- Biological Control Research Institute, Fujian Agriculture and Forestry University, China Fruit Fly Research and Control Center of FAO/IAEA, Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, China
- Lingfei Peng,
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Awan SA, Khan I, Tariq R, Rizwan M, Wang X, Zhang X, Huang L. Genome-Wide Expression and Physiological Profiling of Pearl Millet Genotype Reveal the Biological Pathways and Various Gene Clusters Underlying Salt Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:849618. [PMID: 35419021 PMCID: PMC8996197 DOI: 10.3389/fpls.2022.849618] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/07/2022] [Indexed: 05/04/2023]
Abstract
Pearl millet (Pennisetum glaucum L.) is a vital staple food and an important cereal crop used as food, feed, and forage. It can withstand heat and drought due to the presence of some unique genes; however, the mechanism of salt stress has been missing in pearl millet until now. Therefore, we conducted a comparative transcriptome profiling to reveal the differentially expressed transcripts (DETs) associated with salt stress in pearl millet at different time points, such as 1, 3, and 7 h, of salt treatment. The physiological results suggested that salt stress significantly increased proline, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) in pearl millet at 1, 3, and 7 h of salt treatment. In addition, pearl millet plants regulated the activities of superoxide dismutase, catalase, and peroxidase to lessen the impact of salinity. The transcriptomic results depicted that salt stress upregulated and downregulated the expression of various transcripts involved in different metabolic functions. At 1 and 7 h of salt treatment, most of the transcripts were highly upregulated as compared to the 3 h treatment. Moreover, among commonly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, the mitogen-activated protein kinase (MAPK) signaling pathway and peroxisome pathway were significantly enriched. The DETs related to hormone signaling (auxins, ethylene, gibberellin, and abscisic acid), kinases, protein modifications, and degradation were also identified, depicting the possible role of hormones and kinases to enhance plant tolerance against salt stress. Furthermore, the transcription factors, such as ethylene-responsive element binding factors (ERF), basic helix-loop-helix (bHLH), HMG box-containing protein (HBP), MADS, myeloblastosis (MYB), and WRKY, were predicted to significantly regulate different transcripts involved in salt stress responses at three different time points. Overall, this study will provide new insights to better understand the salt stress regulation mechanisms in pearl millet to improve its resistance against salinity and to identify new transcripts that control these mechanisms in other cereals.
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Affiliation(s)
- Samrah Afzal Awan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rezwan Tariq
- Department of Plant Protection, Akdeniz University, Antalya, Turkey
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Linkai Huang,
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Transcriptome Analysis of Salt Stress in Hibiscus hamabo Sieb. et Zucc Based on Pacbio Full-Length Transcriptome Sequencing. Int J Mol Sci 2021; 23:ijms23010138. [PMID: 35008561 PMCID: PMC8745204 DOI: 10.3390/ijms23010138] [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: 10/08/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022] Open
Abstract
Hibiscus hamabo Sieb. et Zucc is an important semi-mangrove plant with great morphological features and strong salt resistance. In this study, by combining single molecule real time and next-generation sequencing technologies, we explored the transcriptomic changes in the roots of salt stressed H. hamabo. A total of 94,562 unigenes were obtained by clustering the same isoforms using the PacBio RSII platform, and 2269 differentially expressed genes were obtained under salt stress using the Illumina platform. There were 519 differentially expressed genes co-expressed at each treatment time point under salt stress, and these genes were found to be enriched in ion signal transduction and plant hormone signal transduction. We used Arabidopsis thaliana (L.) Heynh. transformation to confirm the function of the HhWRKY79 gene and discovered that overexpression enhanced salt tolerance. The full-length transcripts generated in this study provide a full characterization of the transcriptome of H. hamabo and may be useful in mining new salt stress-related genes specific to this species, while facilitating the understanding of the salt tolerance mechanisms.
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