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Thakur NR, Gorthy S, Vemula A, Odeny DA, Ruperao P, Sargar PR, Mehtre SP, Kalpande HV, Habyarimana E. Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains. Sci Rep 2024; 14:12729. [PMID: 38830906 PMCID: PMC11148041 DOI: 10.1038/s41598-024-63308-0] [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: 12/26/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.
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Affiliation(s)
- Niranjan Ravindra Thakur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - AnilKumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pramod Ramchandra Sargar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | | | - Hirakant V Kalpande
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India.
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Hu C, Nie Z, Shi H, Peng H, Li G, Liu H, Li C, Liu H. Selenium uptake, translocation, subcellular distribution and speciation in winter wheat in response to phosphorus application combined with three types of selenium fertilizer. BMC PLANT BIOLOGY 2023; 23:224. [PMID: 37101116 PMCID: PMC10134582 DOI: 10.1186/s12870-023-04227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Selenium (Se) deficiency causes a series of health disorders in humans, and Se concentrations in the edible parts of crops can be improved by altering exogenous Se species. However, the uptake, transport, subcellular distribution and metabolism of selenite, selenate and SeMet (selenomethionine) under the influence of phosphorus (P) has not been well characterized. RESULTS The results showed that increasing the P application rate enhanced photosynthesis and then increased the dry matter weight of shoots with selenite and SeMet treatment, and an appropriate amount of P combined with selenite treatment increased the dry matter weight of roots by enhancing root growth. With selenite treatment, increasing the P application rate significantly decreased the concentration and accumulation of Se in roots and shoots. P1 decreased the Se migration coefficient, which could be attributed to the inhibited distribution of Se in the root cell wall, but increased distribution of Se in the root soluble fraction, as well as the promoted proportion of SeMet and MeSeCys (Se-methyl-selenocysteine) in roots. With selenate treatment, P0.1 and P1 significantly increased the Se concentration and distribution in shoots and the Se migration coefficient, which could be attributed to the enhanced proportion of Se (IV) in roots but decreased proportion of SeMet in roots. With SeMet treatment, increasing the P application rate significantly decreased the Se concentration in shoots and roots but increased the proportion of SeCys2 (selenocystine) in roots. CONCLUSION Compared with selenate or SeMet treatment, treatment with an appropriate amount of P combined with selenite could promote plant growth, reduce Se uptake, alter Se subcellular distribution and speciation, and affect Se bioavailability in wheat.
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Affiliation(s)
- Caixia Hu
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China
| | - Zhaojun Nie
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China.
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Hongyu Peng
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China
| | - Guangxin Li
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China
| | - Haiyang Liu
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China
| | - Chang Li
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China
| | - Hongen Liu
- Resources and Environment College, Henan Agricultural University, Jinshui District, No. 63, Nongye RoadHenan Province, Zhengzhou, 450002, China.
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Ofori KF, Antoniello S, English MM, Aryee ANA. Improving nutrition through biofortification-A systematic review. Front Nutr 2022; 9:1043655. [PMID: 36570169 PMCID: PMC9784929 DOI: 10.3389/fnut.2022.1043655] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
Nutritious foods are essential for human health and development. However, malnutrition and hidden hunger continue to be a challenge globally. In most developing countries, access to adequate and nutritious food continues to be a challenge. Although hidden hunger is less prevalent in developed countries compared to developing countries where iron (Fe) and zinc (Zn) deficiencies are common. The United Nations (UN) 2nd Sustainable Development Goal was set to eradicate malnutrition and hidden hunger. Hidden hunger has led to numerous cases of infant and maternal mortalities, and has greatly impacted growth, development, cognitive ability, and physical working capacity. This has influenced several countries to develop interventions that could help combat malnutrition and hidden hunger. Interventions such as dietary diversification and food supplementation are being adopted. However, fortification but mainly biofortification has been projected to be the most sustainable solution to malnutrition and hidden hunger. Plant-based foods (PBFs) form a greater proportion of diets in certain populations; hence, fortification of PBFs is relevant in combating malnutrition and hidden hunger. Agronomic biofortification, plant breeding, and transgenic approaches are some currently used strategies in food crops. Crops such as cereals, legumes, oilseeds, vegetables, and fruits have been biofortified through all these three strategies. The transgenic approach is sustainable, efficient, and rapid, making it suitable for biofortification programs. Omics technology has also been introduced to improve the efficiency of the transgenic approach.
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Affiliation(s)
- Kelvin F. Ofori
- Department of Human Ecology, Delaware State University, Dover, DE, United States
| | - Sophia Antoniello
- Department Human Nutrition, Saint Francis Xavier University, Antigonish, NS, Canada
| | - Marcia M. English
- Department Human Nutrition, Saint Francis Xavier University, Antigonish, NS, Canada
| | - Alberta N. A. Aryee
- Department of Human Ecology, Delaware State University, Dover, DE, United States,*Correspondence: Alberta N. A. Aryee,
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Aguilera-Velázquez JR, Calleja A, Moreno I, Bautista J, Alonso E. Metallic profiles and health risk assessment of the most consumed rice varieties in Spain. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.105101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Imran M, Shafiq S, Ilahi S, Ghahramani A, Bao G, Dessoky ES, Widemann E, Pan S, Mo Z, Tang X. Post-transcriptional regulation of 2-acetyl-1-pyrroline (2-AP) biosynthesis pathway, silicon, and heavy metal transporters in response to Zn in fragrant rice. FRONTIERS IN PLANT SCIENCE 2022; 13:948884. [PMID: 36061781 PMCID: PMC9428631 DOI: 10.3389/fpls.2022.948884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulates 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcript variability and proteome diversity in plants. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed based on RNA-seq analysis. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular processes in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars and Zn treatment altered the editing frequency of single nucleotide polymorphism (SNPs) in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Similar to the 2-AP pathway, we found that heavy metal transporters (genes related to silicon, iron, Zn and other metal transport) are also regulated at transcriptional and post-transcriptional levels in response to Zn in fragrant rice. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway and heavy metal transporters may also be regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis and regulation of heavy metal transporters in fragrant rice.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Sara Ilahi
- Department of Economics, Lahore College for Women University, Lahore, Pakistan
| | - Alireza Ghahramani
- Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada
| | - Gegen Bao
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Eldessoky S. Dessoky
- Department of Plant Genetic Transformation, Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Emilie Widemann
- Institut de Biologie Moléculaire des Plantes, CNRS-Université de Strasbourg, Strasbourg, France
| | - Shenggang Pan
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Zhaowen Mo
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
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Transcriptomics View over the Germination Landscape in Biofortified Rice. Genes (Basel) 2021; 12:genes12122013. [PMID: 34946962 PMCID: PMC8700799 DOI: 10.3390/genes12122013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/29/2022] Open
Abstract
Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.
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