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Mazumder AK, Yadav R, Kumar M, Babu P, Kumar N, Singh SK, Solanke AU, Wani SH, Alalawy AI, Alasmari A, Gaikwad KB. Discovering novel genomic regions explaining adaptation of bread wheat to conservation agriculture through GWAS. Sci Rep 2024; 14:16351. [PMID: 39013994 PMCID: PMC11252282 DOI: 10.1038/s41598-024-66903-3] [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: 03/04/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
To sustainably increase wheat yield to meet the growing world population's food demand in the face of climate change, Conservation Agriculture (CA) is a promising approach. Still, there is a lack of genomic studies investigating the genetic basis of crop adaptation to CA. To dissect the genetic architecture of 19 morpho-physiological traits that could be involved in the enhanced adaptation and performance of genotypes under CA, we performed GWAS to identify MTAs under four contrasting production regimes viz., conventional tillage timely sown (CTTS), conservation agriculture timely sown (CATS), conventional tillage late sown (CTLS) and conservation agriculture late sown (CALS) using an association panel of 183 advanced wheat breeding lines along with 5 checks. Traits like Phi2 (Quantum yield of photosystem II; CATS:0.37, CALS: 0.31), RC (Relative chlorophyll content; CATS:55.51, CALS: 54.47) and PS1 (Active photosystem I centers; CATS:2.45, CALS: 2.23) have higher mean values in CA compared to CT under both sowing times. GWAS identified 80 MTAs for the studied traits across four production environments. The phenotypic variation explained (PVE) by these QTNs ranged from 2.15 to 40.22%. Gene annotation provided highly informative SNPs associated with Phi2, NPQ (Quantum yield of non-photochemical quenching), PS1, and RC which were linked with genes that play crucial roles in the physiological adaptation under both CA and CT. A highly significant SNP AX94651261 (9.43% PVE) was identified to be associated with Phi2, while two SNP markers AX94730536 (30.90% PVE) and AX94683305 (16.99% PVE) were associated with NPQ. Identified QTNs upon validation can be used in marker-assisted breeding programs to develop CA adaptive genotypes.
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Affiliation(s)
- Amit Kumar Mazumder
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manjeet Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prashanth Babu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Naresh Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sanjay Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shabir H Wani
- Mountain Research Centre for Field Crops, Khudwani, 192101, India
- Sher-E-Kashmir University of Agricultural Sciences and Technology-Kashmir (SKUAST-K), Srinagar, Jammu-Kashmir, India
| | - Adel I Alalawy
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdulrahman Alasmari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Kiran B Gaikwad
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Bhatla SC, Gogna M, Jain P, Singh N, Mukherjee S, Kalra G. Signaling mechanisms and biochemical pathways regulating pollen-stigma interaction, seed development and seedling growth in sunflower under salt stress. PLANT SIGNALING & BEHAVIOR 2021; 16:1958129. [PMID: 34429013 PMCID: PMC8526035 DOI: 10.1080/15592324.2021.1958129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/04/2023]
Abstract
Sunflower (Helianthus annuus L.) is one of the major oilseed crops cultivated world over for its high-quality oil rich in linoleic acid. It also has established applications in pharmaceutical and biotechnological industries, mainly through recombinant production of unique oil body (OB) membrane proteins-oleosins, which are used for producing a wide variety of vaccines, food products, cosmetics and nutraceuticals. The present review provides a critical analysis of the progress made in advancing our knowledge in sunflower biology, ranging from mechanisms of pollen-stigma interaction, seed development, physiology of seed germination and seedling growth under salt stress, and finally understanding the signaling routes associated with various biochemical pathways regulating seedling growth. Role of nitric oxide (NO) triggered post-translational modifications (PTMs), discovered in the recent past, have paved way for future research directions leading to further understanding of sunflower developmental physiology. Novel protocols recently developed to monitor temporal and spatial distributions of various biochemicals involved in above-stated developmental events in sunflower, will go a long way for similar applications in plant biology in future.
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Affiliation(s)
| | - Mansi Gogna
- Department of Botany, University of Delhi, Delhi, India
| | - Prachi Jain
- Department of Botany, University of Delhi, Delhi, India
| | - Neha Singh
- Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, Jangipur, West Bengal, India
| | - Geetika Kalra
- Department of Botany , Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
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Barnes AC, Elowsky CG, Roston RL. An Arabidopsis protoplast isolation method reduces cytosolic acidification and activation of the chloroplast stress sensor SENSITIVE TO FREEZING 2. PLANT SIGNALING & BEHAVIOR 2019; 14:1629270. [PMID: 31189422 PMCID: PMC6768213 DOI: 10.1080/15592324.2019.1629270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/03/2019] [Indexed: 05/20/2023]
Abstract
Chloroplasts adapt to freezing and other abiotic stresses in part by modifying their membranes. One key-remodeling enzyme is SENSITIVE TO FREEZING2 (SFR2). SFR2 is unusual because it does not respond to initial cold stress or cold acclimation, instead it responds during freezing conditions in Arabidopsis. This response has been shown to be sensitive to cytosolic acidification. The unique lipid products of SFR2 have also been detected in response to non-freezing stresses, but what causes SFR2 to respond in these stresses is unknown. Here, we investigate protoplast isolation as a representative of wounding stress. We show that SFR2 oligogalactolipid products accumulate during protoplast isolation. Notably, we show that protoplast cytosol is acidified during isolation. Modification of the buffers reduces oligogalactolipid accumulation, while prolonged incubation in the isolated state increases it. We conclude that SFR2 activation during protoplast isolation correlates with cytosolic acidification, implying that all SFR2 activation may be dependent on cytosolic acidification. We also conclude that protoplasts can be more gently isolated, reducing their stress.
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Affiliation(s)
- Allison C. Barnes
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Christian G. Elowsky
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca L. Roston
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
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Yu X, Jia D, Duan P. Plasmid engineering of aphid alarm pheromone in tobacco seedlings affects the preference of aphids. PLANT SIGNALING & BEHAVIOR 2019; 14:e1588669. [PMID: 30849285 PMCID: PMC6512937 DOI: 10.1080/15592324.2019.1588669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Plants producing sufficient amount of aphid alarm pheromone by expressing (E)-β-Farnesene (EβF) synthase gene may contribute to plant protection by reducing aphid populations. However, terpene biosynthesis varies among plant species and developmental stages. In the present study, volatile headspace analysis of tobacco seedlings with MaβFS1 (an EβF synthase from the Asian peppermint Mentha asiatica) failed to generate EβF. We further targeted MaβFS1 to the tobacco plastid, using a chloroplast targeting sequence, either with or without the AtFPS1 gene for the biosynthesis of the precursor farnesyl diphosphate. When both MaβFS1 and AtFPS1 genes were targeted to the chloroplast, low levels of EβF were detected in stably transformed tobacco seedlings; resulting in specific repellence of the green peach aphid, Myzus persicae. These data indicate that redirecting the EβF biosynthetic pathway from its natural cytosolic location to the chloroplast is a valid strategy. This redirecting strategy may be very useful for other crop plants that do not naturally produce EβF or other repellent volatiles.
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Affiliation(s)
- Xiudao Yu
- School of Agricultural Engineering/Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, Henan, China
| | - Dianyong Jia
- School of Agricultural Engineering/Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, Henan, China
| | - Pengfei Duan
- School of Agricultural Engineering/Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project, Nanyang Normal University, Nanyang, Henan, China
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Kim H, Kang H, Kwon Y, Choi J, Chang JH. Proportional subcellular localization of Arabidopsis thaliana RabA1a. PLANT SIGNALING & BEHAVIOR 2019; 14:e1581561. [PMID: 30764708 PMCID: PMC6422372 DOI: 10.1080/15592324.2019.1581561] [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: 01/17/2019] [Revised: 02/02/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Subcellular localization of trafficking proteins in a single cell affects the assembly of trafficking machinery between organelles and vesicles throughout the targeting pathway. RabGTPase is one of the regulators to direct specific targeting of cargo molecules depending on GDP/GTP bound status. We have recently determined the crystal structures of GDP-bound inactive and both GTP- and GppNHp-bound active forms of Arabidopsis RabA1a. It is notable that the switch regions of RabA1a exhibit conformational changes derived by GDP or GTP binding. However, it was not clear that where the GDP- or GTP-bound RabA1a is localized at the subcellular level in a cell. Here we demonstrate that the distinct proportion of subcellular localization of RabA1a depends on its site-specific mutation as the GDP- or GTP-bound form. RabA1a proteins located at the plasma membrane, endosomes, and cytosol. While the GDP-bound form of RabA1aS27N located more at endosomes than the plasma membrane compared to the proportions of RabA1a wild-type, and the GTP-bound RabA1aQ72L located mainly at the plasma membrane in comparison to RabA1a wild-type and RabA1aS27N. These distinct proportional localizations of RabA1a enable a cognate interaction between inactive/active RabA1 and effector molecules to direct specific targeting of its cargo molecules.
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Affiliation(s)
- Hyeran Kim
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Hyangju Kang
- Division of Molecular and Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea
| | - Yun Kwon
- Division of Molecular and Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea
- Helmholtz Center Munich, Institute for Diabetes and Cancer, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Jisun Choi
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu, South Korea
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Zhang C, Liu P. The New Face of the Lipid Droplet: Lipid Droplet Proteins. Proteomics 2018; 19:e1700223. [DOI: 10.1002/pmic.201700223] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/13/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Congyan Zhang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Pingsheng Liu
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
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Kutschera U, Niklas KJ. Julius von Sachs' forgotten 1897-article: sexuality and gender in plants vs. humans. PLANT SIGNALING & BEHAVIOR 2018; 13:e1489671. [PMID: 29993309 PMCID: PMC6128683 DOI: 10.1080/15592324.2018.1489671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 05/21/2023]
Abstract
One hundred and fifty years ago, Julius von Sachs' (1832-1897) monumental Lehrbuch der Botanik (Textbook of Botany) was published, which signified the origin of physiological botany and its integration with evolutionary biology. Sachs regarded the physiology of photoautotrophic organisms as a sub-discipline of botany, and introduced a Darwinian perspective into the emerging plant sciences. Here, we summarize Sachs' achievements and his description of sexuality with respect to the cellular basis of plant and animal biparental reproduction. We reproduce and analyze a forgotten paper (Gutachten) of Sachs dealing with Die Akademische Frau (The Academic Woman), published during the year of his death on the question concerning gender equality in humans. Finally, we summarize his endorsement of woman's rights to pursue academic studies in the natural sciences at the University level, and conclude that Sachs was a humanist as well as a great scientist.
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Affiliation(s)
| | - Karl J. Niklas
- Plant Science Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Zhi Y, Taylor MC, Campbell PM, Warden AC, Shrestha P, El Tahchy A, Rolland V, Vanhercke T, Petrie JR, White RG, Chen W, Singh SP, Liu Q. Comparative Lipidomics and Proteomics of Lipid Droplets in the Mesocarp and Seed Tissues of Chinese Tallow ( Triadica sebifera). FRONTIERS IN PLANT SCIENCE 2017; 8:1339. [PMID: 28824675 PMCID: PMC5541829 DOI: 10.3389/fpls.2017.01339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/18/2017] [Indexed: 05/04/2023]
Abstract
Lipid droplets (LDs) are composed of a monolayer of phospholipids (PLs), surrounding a core of non-polar lipids that consist mostly of triacylglycerols (TAGs) and to a lesser extent diacylglycerols. In this study, lipidome analysis illustrated striking differences in non-polar lipids and PL species between LDs derived from Triadica sebifera seed kernels and mesocarp. In mesocarp LDs, the most abundant species of TAG contained one C18:1 and two C16:0 and fatty acids, while TAGs containing three C18 fatty acids with higher level of unsaturation were dominant in the seed kernel LDs. This reflects the distinct differences in fatty acid composition of mesocarp (palmitate-rich) and seed-derived oil (α-linoleneate-rich) in T. sebifera. Major PLs in seed LDs were found to be rich in polyunsaturated fatty acids, in contrast to those with relatively shorter carbon chain and lower level of unsaturation in mesocarp LDs. The LD proteome analysis in T. sebifera identified 207 proteins from mesocarp, and 54 proteins from seed kernel, which belong to various functional classes including lipid metabolism, transcription and translation, trafficking and transport, cytoskeleton, chaperones, and signal transduction. Oleosin and lipid droplets associated proteins (LDAP) were found to be the predominant proteins associated with LDs in seed and mesocarp tissues, respectively. We also show that LDs appear to be in close proximity to a number of organelles including the endoplasmic reticulum, mitochondria, peroxisomes, and Golgi apparatus. This comparative study between seed and mesocarp LDs may shed some light on the structure of plant LDs and improve our understanding of their functionality and cellular metabolic networks in oleaginous plant tissues.
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Affiliation(s)
- Yao Zhi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
- CSIRO Agriculture and FoodCanberra, ACT, Australia
| | | | | | | | | | | | | | | | | | | | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Wenli Chen
| | | | - Qing Liu
- CSIRO Agriculture and FoodCanberra, ACT, Australia
- Qing Liu
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