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Kwon JS, Shilpha J, Lee J, Yeom SI. Beyond NGS data sharing for plant ecological resilience and improvement of agronomic traits. Sci Data 2024; 11:466. [PMID: 38719829 PMCID: PMC11079010 DOI: 10.1038/s41597-024-03305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Decoding complex plant omics is essential for advancing our understanding of plant biology, evolution, and breeding as well as for practical applications in agriculture, conservation, and biotechnology. The advent of Next-Generation Sequencing (NGS) has revolutionized global plant genomic research, offering high-throughput, cost-effective, and accurate methods for generating genomic data. However, challenges still exist that suggest an entirely unresolved genome characterized by high heterozygosity, extensive repetitive sequences, and complex ploidy features. In addition, individual investigation of genomic information from various genetic resources is essential for omics research, as there are differences in traits within a single breed beyond a species due to the uniqueness of sequence variation. This article provides high-quality genomic and transcriptomic insights targeted at the agronomical background.
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Affiliation(s)
- Ji-Su Kwon
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Jayabalan Shilpha
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Seon-In Yeom
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Korea.
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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) 2023; 12:3378. [PMID: 37836117 PMCID: PMC10574462 DOI: 10.3390/plants12193378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 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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Yang J, Song J, Shilpha J, Jeong BR. Top and Side Lighting Induce Morphophysiological Improvements in Korean Ginseng Sprouts ( Panax ginseng C.A. Meyer) Grown from One-Year-Old Roots. Plants (Basel) 2023; 12:2849. [PMID: 37571002 PMCID: PMC10421474 DOI: 10.3390/plants12152849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Nowadays, not only the roots, but also leaves and flowers of ginseng are increasingly popular ingredients in supplements for healthcare products and traditional medicine. The cultivation of the shade-loving crop, ginseng, is very demanding in terms of the light environment. Along with the intensity and duration, light direction is another important factor in regulating plant morphophysiology. In the current study, three lighting directions-top (T), side (S), or top + side (TS)-with an intensity of 30 ± 5 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) were employed. Generally, compared with the single T lighting, the composite lighting direction, TS, was more effective in shaping the ginseng with improved characteristics, including shortened, thick shoots; enlarged, thick leaves; more leaf trichomes; earlier flower bud formation; and enhanced photosynthesis. The single S light resulted in the worst growth parameters and strongly inhibited the flower bud formation, leading to the latest flower bud observation. Additionally, the S lighting acted as a positive factor in increasing the leaf thickness and number of trichomes on the leaf adaxial surface. However, the participation of the T lighting weakened these traits. Overall, the TS lighting was the optimal direction for improving the growth and development traits in ginseng. This preliminary research may provide new ideas and orientations in ginseng cultivation lodging resistance and improving the supply of ginseng roots, leaves, and flowers to the market.
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Affiliation(s)
- Jingli Yang
- Shandong Facility Horticulture Bioengineering Research Center, Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang 262700, China; (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinnan Song
- Shandong Facility Horticulture Bioengineering Research Center, Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang 262700, China; (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jayabalan Shilpha
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Byoung Ryong Jeong
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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Muthuramalingam P, Muthamil S, Shilpha J, Venkatramanan V, Priya A, Kim J, Shin Y, Chen JT, Baskar V, Park K, Shin H. Molecular Insights into Abiotic Stresses in Mango. Plants (Basel) 2023; 12:1939. [PMID: 37653856 PMCID: PMC10224100 DOI: 10.3390/plants12101939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/19/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Mango (Mangifera indica L.) is one of the most economically important fruit crops across the world, mainly in the tropics and subtropics of Asia, Africa, and Central and South America. Abiotic stresses are the prominent hindrance that can adversely affect the growth, development, and significant yield loss of mango trees. Understanding the molecular physiological mechanisms underlying abiotic stress responses in mango is highly intricate. Therefore, to gain insights into the molecular basis and to alleviate the abiotic stress responses to enhance the yield in the mere future, the use of high-throughput frontier approaches should be tied along with the baseline investigations. Taking these gaps into account, this comprehensive review mainly speculates to provide detailed mechanisms and impacts on physiological and biochemical alterations in mango under abiotic stress responses. In addition, the review emphasizes the promising omics approaches in unraveling the candidate genes and transcription factors (TFs) responsible for abiotic stresses. Furthermore, this review also summarizes the role of different types of biostimulants in improving the abiotic stress responses in mango. These studies can be undertaken to recognize the roadblocks and avenues for enhancing abiotic stress tolerance in mango cultivars. Potential investigations pointed out the implementation of powerful and essential tools to uncover novel insights and approaches to integrate the existing literature and advancements to decipher the abiotic stress mechanisms in mango. Furthermore, this review serves as a notable pioneer for researchers working on mango stress physiology using integrative approaches.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (P.M.); (J.S.)
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (J.K.); (Y.S.)
| | - Subramanian Muthamil
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea;
| | - Jayabalan Shilpha
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (P.M.); (J.S.)
| | | | - Arumugam Priya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA;
| | - Jinwook Kim
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (J.K.); (Y.S.)
| | - Yunji Shin
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (J.K.); (Y.S.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
| | - Venkidasamy Baskar
- Department of Oral and Maxillofacial Surgery, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospitals, Saveetha University, Chennai 600077, India;
| | - Kyoungmi Park
- Department of Horticulture Research, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju 52733, Republic of Korea;
| | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (P.M.); (J.S.)
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Republic of Korea; (J.K.); (Y.S.)
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Shilpha J, Meyappan V, Sakthivel N. Bioinspired synthesis of gold nanoparticles from Hemidesmus indicus L. root extract and their antibiofilm efficacy against Pseudomonas aeruginosa. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sohn SI, Pandian S, Rakkammal K, Largia MJV, Thamilarasan SK, Balaji S, Zoclanclounon YAB, Shilpha J, Ramesh M. Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview. Front Plant Sci 2022; 13:942789. [PMID: 36035665 PMCID: PMC9407636 DOI: 10.3389/fpls.2022.942789] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.
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Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | | | - Senthil Kumar Thamilarasan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | - Yedomon Ange Bovys Zoclanclounon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jayabalan Shilpha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
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Largia MJV, Satish L, Johnsi R, Shilpha J, Ramesh M. Analysis of propagation of Bacopa monnieri (L.) from hairy roots, elicitation and Bacoside A contents of Ri transformed plants. World J Microbiol Biotechnol 2016; 32:131. [DOI: 10.1007/s11274-016-2083-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
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Satish L, Shilpha J, Pandian S, Rency AS, Rathinapriya P, Ceasar SA, Largia MJV, Kumar AA, Ramesh M. Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods. Gene 2016; 576:581-5. [DOI: 10.1016/j.gene.2015.10.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
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