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Maharajan T, Krishna TPA, Shilpha J, Ceasar SA. Effects of Individual or Combined Deficiency of Phosphorous and Zinc on Phenotypic, Nutrient Uptake, and Molecular Responses of Finger Millet ( Eleusine coracana): A Nutri-Rich Cereal Crop. PLANTS (BASEL, SWITZERLAND) 2023; 12:3378. [PMID: 37836117 PMCID: PMC10574462 DOI: 10.3390/plants12193378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Deficiencies of either phosphorus (P) or zinc (Zn) or both are one of the major abiotic constraints influencing agricultural production. Research on the effects of individual or combined P and Zn deficiency is limited in cereals. This study reports the effects of the individual or combined deficiency of inorganic phosphate (Pi) and Zn on the phenotypic, root hair modification, nutrient uptake, and molecular responses of finger millet (Eleusine coracana), a nutri-rich cereal crop. Finger millet seedlings were grown hydroponically under control (+Pi+Zn), individual Pi deficiency (-Pi), individual Zn deficiency (-Zn), and combined Pi and Zn deficiency (-Pi-Zn) conditions for 30 days to find the phenotypic, root hair modification, nutrient uptake, and molecular responses. Compared to the individual -Zn condition, the individual -Pi condition had more of an effect in terms of biomass reduction. The combined -Pi-Zn condition increased the root hair length and density compared to the other three conditions. The individual -Zn condition increased the Pi uptake, while the individual -Pi condition favored the Zn uptake. EcZIP2 was highly upregulated in shoot tissues under the individual -Zn condition, and EcPHT1;2 was highly expressed in root tissues under the individual -Pi condition. This is the first study to report the effects of the individual or combined deficiency of Pi and Zn in finger millet and may lead to future studies to better manage P and Zn deficiency.
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Affiliation(s)
- Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin 683104, India; (T.M.); (T.P.A.K.)
| | | | - Jayabalan Shilpha
- Department of Horticulture, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin 683104, India; (T.M.); (T.P.A.K.)
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Xing G, Jin M, Yue P, Ren C, Hao J, Zhao Y, Zhao X, Sun Z, Hou S. Role of SiPHR1 in the Response to Low Phosphate in Foxtail Millet via Comparative Transcriptomic and Co-Expression Network Analyses. Int J Mol Sci 2023; 24:12786. [PMID: 37628968 PMCID: PMC10454940 DOI: 10.3390/ijms241612786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Enhancing the absorption and utilization of phosphorus by crops is an important aim for ensuring food security worldwide. However, the gene regulatory network underlying phosphorus use in foxtail millet remains unclear. In this study, the molecular mechanism underlying low-phosphorus (LP) responsiveness in foxtail millet was evaluated using a comparative transcriptome analysis. LP reduced the chlorophyll content in shoots, increased the anthocyanin content in roots, and up-regulated purple acid phosphatase and phytase activities as well as antioxidant systems (CAT, POD, and SOD). Finally, 13 differentially expressed genes related to LP response were identified and verified using transcriptomic data and qRT-PCR. Two gene co-expression network modules related to phosphorus responsiveness were positively correlated with POD, CAT, and PAPs. Of these, SiPHR1, functionally annotated as PHOSPHATE STARVATION RESPONSE 1, was identified as an MYB transcription factor related to phosphate responsiveness. SiPHR1 overexpression in Arabidopsis significantly modified the root architecture. LP stress caused cellular, physiological, and phenotypic changes in seedlings. SiPHR1 functioned as a positive regulator by activating downstream genes related to LP tolerance. These results improve our understanding of the molecular mechanism underlying responsiveness to LP stress, thereby laying a theoretical foundation for the genetic modification and breeding of new LP-tolerant foxtail millet varieties.
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Affiliation(s)
- Guofang Xing
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan 030031, China
| | - Minshan Jin
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
| | - Peiyao Yue
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
| | - Chao Ren
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
| | - Jiongyu Hao
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
| | - Yue Zhao
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
| | - Xiongwei Zhao
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan 030031, China
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Zhaoxia Sun
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan 030031, China
| | - Siyu Hou
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (G.X.); (M.J.); (Z.S.)
- Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan 030031, China
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Chang OC, Lin WY. Variation of growth and transcriptome responses to arbuscular mycorrhizal symbiosis in different foxtail millet lines. BOTANICAL STUDIES 2023; 64:16. [PMID: 37326894 DOI: 10.1186/s40529-023-00391-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) have been applied to promote the growth of different crop species, but knowledge about the impacts of symbiosis on foxtail millet at the physiological and molecular levels have remained limited. In this study, we compared the mycorrhization phenotypes of one cultivar and three different landraces and performed a comprehensive transcriptomic analysis to assess the effects of genetic variation on the responses to symbiosis. RESULTS Our results showed that colonization by AMF did not enhance biomass accumulation but significantly increased grain production only in three lines. More than 2,000 genes were affected by AMF colonization in all lines. Most AM symbiosis-conserved genes were induced, but the induction levels varied between lines. Gene Ontology (GO) analysis showed that Biological Function terms related to nitrogen transport and assimilation were only enriched in TT8. Similarly, two of phosphate starvation-induced phosphate transporters were only simultaneously downregulated in TT8. In the other two lines, the enrichment of GO terms associated with cell wall reorganization and lignification was observed, though the effects were different. CONCLUSION This study reveals the impacts of genetic variation of millet lines on the responses to AM symbiosis and provides information regarding AMF application for millet production.
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Affiliation(s)
- Ou-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, 106319, Taiwan
| | - Wei-Yi Lin
- Department of Agronomy, National Taiwan University, Taipei, 106319, Taiwan.
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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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Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim YM, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, Callister SJ. Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil. PLoS One 2021; 16:e0259937. [PMID: 34879068 PMCID: PMC8654227 DOI: 10.1371/journal.pone.0259937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.
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Affiliation(s)
- Matthew J. Peterson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pubudu P. Handakumbura
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Allison M. Thompson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Zachary R. Russell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Sarah J. Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Montana L. Smith
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason G. Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rosey K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bryan A. Stanfill
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Steven C. Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington, United States of America
| | - Vanessa L. Bailey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (SJC); (KKH)
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Yang Y, Zhu X, Cui R, Wang R, Li H, Wang J, Chen H, Zhang D. Identification of soybean phosphorous efficiency QTLs and genes using chlorophyll fluorescence parameters through GWAS and RNA-seq. PLANTA 2021; 254:110. [PMID: 34716824 DOI: 10.1007/s00425-021-03760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
MAIN CONCLUSION Soybean phosphorous efficiency QTLs were identified and candidate genes were predicted using chlorophyll fluorescence parameters through GWAS and RNA-seq. Phosphorus (P) is an essential nutrient element for crop growth and development, lack of P uptake seriously affects yield in various crops. Photosynthesis is the basis of crop production, while it is very sensitive to P deficiency. It is of great importance to study the genetic relationship between photosynthesis and P efficiency to provide genetic insight for soybean improvement. In this study, a genome-wide association study (GWAS) was performed using 292,035 SNPs and the ratios of four main chlorophyll fluorescence parameters of 219 diverse soybean accessions under P deficiency and normal P across three experiments. In total, 52 SNPs in 12 genomic regions were detected in association with the four main chlorophyll fluorescence parameters under sufficient or deficient P levels. Combined it with RNA-seq analysis, we predicted three candidate genes for the significant genomic regions. For example, the expression level of the candidate gene (Glyma.18g092900) in P deficiency tolerant accession was three times higher than that of P deficiency sensitive one under phosphorous deficiency condition. This study provides insight into genetic links between photosynthetic and phosphorous efficiency and further functional analysis will provide valuable information for understanding the underlying genetic mechanism to facilitate marker-assisted breeding in soybean.
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Affiliation(s)
- Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Xiuhua Zhu
- Henan Xuke Seed Industry Co., Ltd, Xuchang, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China.
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Roch GV, Maharajan T, Krishna TPA, Ignacimuthu S, Ceasar SA. Expression of PHT1 family transporter genes contributes for low phosphate stress tolerance in foxtail millet (Setaria italica) genotypes. PLANTA 2020; 252:98. [PMID: 33159589 DOI: 10.1007/s00425-020-03503-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/23/2020] [Indexed: 05/27/2023]
Abstract
This is a first comprehensive study to analyze the 12 PHT1 family phosphate transporter genes in 20 foxtail millet genotypes for the improvement of millets and other crops for phosphate use efficiency. Phosphorus (P), absorbed from soil solutions as inorganic phosphate (Pi), is a limiting nutrient for plant growth and yield. Twenty genotypes of foxtail millet (Setaria italica) with contrasting degree of growth and Pi uptake responses under low Pi (LP) and high Pi (HP) supply were chosen based on a previous study. To gain molecular insights, expression dynamics of 12 PHosphate Transporter 1 (PHT1) family (SiPHT1;1 to 1;12) genes were analyzed in these 20 genotypes and compared with their Pi and total P (TP) contents. SiPHT1;1, 1;2, 1;3 and 1;8 genes were expressed in shoot tissues of three (ISe 1209, ISe 1305 and Co-6) of the LP best performing genotypes (LPBG); however, they were expressed in only one of the LP worst performing genotype (LPWG) (ISe 748). More importantly, this is correlating with higher shoot Pi and TP contents of the LPBG compared to LPWG. Apart from this condition, expression of SiPHT1 genes and their Pi and TP contents do not correlate directly for many genotypes in other conditions; genotypes with low Pi and TP contents induced more SiPHT1 genes and vice versa. Promoter analysis revealed that genotype ISe 1888 with a high level of SiPHT1;8 expression possesses two additional root box motifs compared to other genotypes. The PHT1 family genes seem to play a key role for LP stress tolerance in foxtail millet and further studies will help to improve the P-use efficiency in foxtail millet and other cereals.
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Affiliation(s)
- G Victor Roch
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - T Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - T P Ajeesh Krishna
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - S Ignacimuthu
- Xavier Research Foundation, St Xavier's College, Palayamkottai, India
| | - S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India.
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