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Kayastha S, Sahoo JP, Mahapatra M, Sharma SS. Finger millet (Eleusine coracana) enhancement through genomic resources and breeding methods: current implications and potential future interventions. PLANTA 2024; 259:139. [PMID: 38687379 DOI: 10.1007/s00425-024-04415-0] [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: 02/24/2024] [Accepted: 04/14/2024] [Indexed: 05/02/2024]
Abstract
Finger millet (Eleusine coracana) is an essential staple crop in many regions of Africa and Asia, valued for its nutritional content and resilience in challenging agro-ecological conditions. The enhancement of finger millet through genomic resources and breeding methods represents a promising avenue for addressing food and nutritional security. Current efforts in this field have harnessed genomic technologies to decipher the crop's genetic diversity and identify key traits related to yield, disease resistance, and nutritional content. These insights have facilitated the development of improved varieties through selective breeding, accelerating the crop's adaptation to changing environmental conditions. In the future, continued advancements in genomics and breeding methodologies hold the potential to further enhance finger millet's resilience, nutritional value, and productivity, ultimately benefiting both farmers and consumers. This review article synthesizes the current state of research and development in finger millet enhancement through the integration of genomic resources and innovative breeding methods. The utilization of these insights in selective breeding has already yielded promising results in developing improved finger millet varieties that meet the evolving needs of farmers and consumers. Moreover, this article discusses potential future interventions, including the continued advancement of genomics, precision breeding, and sustainable agricultural practices. These interventions hold the promise of further enhancing finger millet's adaptability to changing climates, its nutritional quality, and its overall productivity, thereby contributing to food security and improved livelihoods in finger millet-dependent regions.
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Affiliation(s)
- Salma Kayastha
- Faculty of Agriculture and Allied Sciences, C.V. Raman Global University, Bhubaneswar, 752054, India
| | - Jyoti Prakash Sahoo
- Faculty of Agriculture and Allied Sciences, C.V. Raman Global University, Bhubaneswar, 752054, India.
| | - Manaswini Mahapatra
- Faculty of Agriculture and Allied Sciences, C.V. Raman Global University, Bhubaneswar, 752054, India
| | - Siddhartha Shankar Sharma
- Faculty of Agriculture and Allied Sciences, C.V. Raman Global University, Bhubaneswar, 752054, India
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Teklu D, Gashu D, Joy EJM, Bailey EH, Wilson L, Amede T, Broadley MR. Differences in the nutritional quality of improved finger millet genotypes in Ethiopia. Sci Rep 2024; 14:460. [PMID: 38172143 PMCID: PMC10764915 DOI: 10.1038/s41598-023-48749-3] [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: 03/20/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Improved crop genotypes are constantly introduced. However, information on their nutritional quality is generally limited. The present study reports the proximate composition and the concentration and relative bioavailability of minerals of improved finger millets of different genotypes. Grains of finger millet genotypes (n = 15) grown in research station during 2019 and 2020 in Ethiopia, and replicated three times in a randomized complete block design, were analysed for proximate composition, mineral concentration (iron, zinc, calcium, selenium), and antinutritional factors (phytate, tannin and oxalate). Moreover, the antinutritional factors to mineral molar ratio method was used to estimate mineral bioavailability. The result shows a significant genotypic variation in protein, fat and fibre level, ranging from 10% to 14.6%, 1.0 to 3.8%, and 1.4 to 4.6%, respectively. Similarly, different finger millets genotypes had significantly different mineral concentrations ranging from 3762 ± 332 to 5893 ± 353 mg kg-1 for Ca, 19.9 ± 1.6 to 26.2 ± 2.7 mg kg-1 for Zn, 36.3 ± 4.6 to 52.9 ± 9.1 mg kg-1 for Fe and 36.6 ± 11 to 60.9 ± 22 µg kg-1 for Se. Phytate (308-360 µg g-1), tannin (0.15-0.51 mg g-1) and oxalate (1.26-4.41 mg g-1) concentrations were also influenced by genotype. Antinutritional factors to minerals molar ratio were also significantly different by genotypes but were below the threshold for low mineral bioavailability. Genotype significantly influenced mineral and antinutritional concentrations of finger millet grains. In addition, all finger millet genotypes possess good mineral bioavailability. Especially, the high Ca concentration in finger millet, compared to in other cereals, could play a vital role to combating Ca deficiency. The result suggests the different finger millet genotypes possess good nutrient content and may contribute to the nutrition security of the local people.
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Affiliation(s)
- Demeke Teklu
- Center for Food Science and Nutrition, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dawd Gashu
- Center for Food Science and Nutrition, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Edward J M Joy
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Elizabeth H Bailey
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Lolita Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Tilahun Amede
- Alliance for a Green Revolution in Africa (AGRA), Sustainably Growing Africa's Food Systems, Nairobi, Kenya
| | - Martin R Broadley
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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Backiyalakshmi C, Vetriventhan M, Deshpande S, Babu C, Allan V, Naresh D, Gupta R, Azevedo VCR. Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank. FRONTIERS IN PLANT SCIENCE 2021; 12:692463. [PMID: 34489996 PMCID: PMC8417690 DOI: 10.3389/fpls.2021.692463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 - 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.
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Affiliation(s)
- C. Backiyalakshmi
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C. Babu
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - V. Allan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - D. Naresh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vania C. R. Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Molecular Characterization and Positive Impact of Brassinosteroids and Chitosan on Solidago canadensis cv. Tara Characteristics. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although goldenrod (Solidago canadensis) is considered an invasive plant in many countries, it is a global cut-flower species. In addition, demand for goldenrod has increased significantly in recent years. Thus, the present study aimed to evaluate the response of Solidago canadensis cv. Tara to brassinosteroids (BRs) at levels of 0.10−3, 10−6, and 10−8 M, and chitosan at 0, 100, 150, and 200 mg/L as a foliar application to increase the quality and quantity of production, and its polyphenolic compounds. Moreover, antibacterial activity and genetic polymorphism for both untreated and the optimally treated goldenrod were investigated. The results showed that the highest mean of growth characteristics was found when plants were treated with BRs at 10−8 M, whereas the longer vase life was obtained using 200 mg/L chitosan. Furthermore, higher pigment values, N, P, K, and total phenolic content, antioxidant capacity, chlorogenic acid, and rutin content were detected on plants treated with 200 mg/L chitosan. In addition, foliar application with 200 mg/L chitosan caused higher antibacterial activity among the control and BRs. The optimal treatment of BR at 10−8 M (89%) showed a low genetic similarity, based on sequence-related amplified polymorphism (SRAP) analysis, comparable with the control and 200 mg/L chitosan. BR at 10−8 M and 200 mg/L chitosan showed a significant enhancement of growth parameters. As a result, it can be concluded that goldenrod, as a herb extract, shows significant promise as a natural preservative in pharmaceutical, food, and cosmetic products.
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Ravi RSD, Siril EA, Nair BR. The efficiency of Cytochrome P450 gene-based markers in accessing genetic variability of drumstick (Moringa oleifera Lam.) accessions. Mol Biol Rep 2020; 47:2929-2939. [PMID: 32236894 DOI: 10.1007/s11033-020-05391-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/24/2020] [Indexed: 11/24/2022]
Abstract
Drumstick (Moringa oleifera Lam.) is an important vegetable as well as forage crop of arid and semi-arid zones of the tropics. The leaves and pods of the plant are rich sources of minerals and vitamins. In the present work, genetic diversity study of 23 genotypes of M. oleifera collected from Kerala, Tamil Nadu and Karnataka states of India was carried out using seven cytochrome P450 (CytP450) markers. By using seven pairs of CytP450 gene-based markers, 88.25% of polymorphism was recorded among the 23 sampled genotypes. The Polymorphic Information Content (PI), Marker Index (MI) and Resolving Power obtained for seven primers were estimated 0.23, 2.96 and 9.83, respectively. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram based on this marker data indicate that genotypes from different geographical regions are placed in the same clusters. The dendrogram and Principal Coordinates Analysis (PCoA) plots derived from the binary data matrices were highly concordant. The investigation, in brief, proved that CytP450 based marker system is efficient in the elucidation of genetic diversity in M. oleifera accessions.
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Affiliation(s)
- R S Drisya Ravi
- Department of Biotechnology, University of Kerala, Kariavattom, Trivandrum, 695581, India
| | - E A Siril
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India.
| | - Bindu R Nair
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India
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Avashthi H, Pathak RK, Pandey N, Arora S, Mishra AK, Gupta VK, Ramteke PW, Kumar A. Transcriptome-wide identification of genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada pathway) and related pathway for elucidating its role in antioxidative potential in finger millet ( Eleusine coracana (L.)). 3 Biotech 2018; 8:499. [PMID: 30498672 DOI: 10.1007/s13205-018-1511-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022] Open
Abstract
Finger millet is being recognized as a potential future crop due to their nutrient contents and antioxidative properties, which are much higher compared to the other minor millets for providing health benefits. The synthesis of these nutritional components is governed by the expression of several gene(s). Therefore, it is necessary to characterize these genes for understanding the molecular mechanisms behind de novo synthesis of nutrient components. Apart from this, these important compounds could also serve as candidate genes for imparting stress tolerance in other crop plants also. In the present study, effort has been made to identify genes involved in Ascorbate-Glutathione cycle (Halliwell-Asada Pathway) and related pathway genes for elucidating its role in antioxidative potential mechanism through transcriptome data analysis. APX, DHAR, MDHAR, GR, and SOD have been identified as the key genes of the pathway in two genotypes GP-1 (low Ca2+) and GP-45 (high Ca2+) of finger millet with reference to rice as a model system, besides, 30 putatively expressed genes/proteins were also investigated. Furthermore, the sequences of identified genes were analyzed systematically; gene ontology (GO) annotation and enrichment analysis of assembled unitranscripts were also performed using Blast2GO. As a result, 49 GO terms, 5 Enzyme Commission (EC) numbers, and 2 KEGG pathway maps were generated. GO results revealed that these genes are mainly involved in two biological processes (BP), viz., oxidation-reduction process (GO:0055114) and cellular oxidant detoxification (GO:0098869), and showed oxidoreductase activity (GO:0016491). KEGG analysis showed that APX, DHAR, MDHAR, and GR are directly connected to biosynthetic pathways of secondary metabolites, mainly polyphenolic compounds (flavonoid, tannin, and lignin) involved in glutathione metabolism (KEGG:00480) and ascorbate and aldarate metabolism (KEGG:00053). While SOD, is indirectly connected and also has significant medicinal attributes and antioxidant properties. Moreover, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were also calculated for expression analysis and found that the FPKM values of genes present in GP-1 are higher than that of GP-45. Thus, GP-1 genotype was found to have higher stress regulated gene expression in comparison to GP-45. Taken together, the present transcriptome-based investigation unlocks new avenues for systematic functional analysis of novel ROS scavenging candidate genes that could be effectively applied for improvising human health and nutrition.
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Affiliation(s)
- Himanshu Avashthi
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh India
- 2Agricultural Knowledge Management Unit, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi India
| | - Rajesh Kumar Pathak
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand India
- 4Present Address: School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab India
| | - Neetesh Pandey
- 5Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi India
| | - Sandeep Arora
- 6Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand India
| | - Amrendra Kumar Mishra
- 2Agricultural Knowledge Management Unit, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi India
| | - Vijai Kumar Gupta
- 7Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Pramod Wasudeo Ramteke
- Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh India
| | - Anil Kumar
- 6Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh India
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Microsatellite markers of finger millet (Eleusine coracana (L.) Gaertn) and foxtail millet (Setaria italica (L.) Beauv) provide resources for cross-genome transferability and genetic diversity analyses in other millets. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
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Prabhu KS, Das AB, Dikshit N. Assessment of genetic diversity in ragi [Eleusine coracana (L.) Gaertn] using morphological, RAPD and SSR markers. Z NATURFORSCH C 2018; 73:165-176. [PMID: 29654693 DOI: 10.1515/znc-2017-0182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 02/28/2018] [Indexed: 11/15/2022]
Abstract
Finger millet (Eleusine coracana L. Gaertn., 2n=36) is one of the most important minor crops, commonly known as 'ragi' and used as a staple food grain in more than 25 countries including Africa and south Asia. Twenty-seven accessions of ragi were collected from different parts of India and were evaluated for morpho-genetic diversity studies. Simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers were used for assessment of genetic diversity among 27 genotypes of E. coracana. High degree of similarity (90%) was obtained between 'IC49979A' and 'IC49974B' genotypes, whereas low level of similarity (9.09%) was found between 'IC204141' and 'IC49985' as evident in morphological and DNA markers. A total of 64 SSR and 301 RAPD amplicons were produced, out of which 87.50% and 77.20% DNA fragments showed polymorphism, respectively. The clustering pattern obtained among the genotypes corresponded well with their morphological and cytological data with a monophyletic origin of this species which was further supported by high bootstrap values and principal component analysis. Cluster analysis showed that ragi accessions were categorised into three distinct groups. Genotypes IC344761, IC340116, IC340127, IC49965 and IC49985 found accession specific in RAPD and SSR markers. The variation among ragi accessions might be used as potential source of germplasm for crop improvement.
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Affiliation(s)
- Kalapad Santosh Prabhu
- Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Orissa, India
| | - Anath Bandhu Das
- Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Orissa, India.,Post Graduate Department of Botany, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Nilamani Dikshit
- NBPGR Regional Station, Dr. PDKV Campus, Akola 444104, Maharastra, India
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Akbar N, Gupta S, Tiwari A, Singh K, Kumar A. Characterization of metabolic network of oxalic acid biosynthesis through RNA seq data analysis of developing spikes of finger millet ( Eleusine coracana ): Deciphering the role of key genes involved in oxalate formation in relation to grain calcium accumulation. Gene 2018; 649:40-49. [DOI: 10.1016/j.gene.2018.01.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 12/11/2017] [Accepted: 01/22/2018] [Indexed: 01/19/2023]
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Molecular characterization of EcCIPK24 gene of finger millet ( Eleusine coracana) for investigating its regulatory role in calcium transport. 3 Biotech 2017; 7:267. [PMID: 28794922 DOI: 10.1007/s13205-017-0874-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/07/2017] [Indexed: 10/19/2022] Open
Abstract
Finger millet grains contain exceptionally high levels of calcium which is much higher compared to other cereals and millets. Since calcium is an important macronutrient in human diet, it is necessary to explore the molecular basis of calcium accumulation in the seeds of finger millet. CIPK is a calcium sensor gene, having role in activating Ca2+ exchanger protein by interaction with CBL proteins. To know the role of EcCIPK24 gene in seed Ca2+ accumulation, sequence is retrieved from the transcriptome data of two finger millet genotypes GP1 (low Ca2+) and GP45 (high Ca2+), and the expression was determined through qRT-PCR. The higher expression was found in root, shoot, leaf and developing spike tissue of GP45 compared to GP1; structural analysis showed difference of nine SNPs and one extra beta sheet domain as well as differences in vacuolar localization was predicted; besides, the variation in amino acid composition among both the genotypes was also investigated. Molecular modeling and docking studies revealed that both EcCBL4 and EcCBL10 showed strong binding affinity with EcCIPK24 (GP1) compared to EcCIPK24 (GP45). It indicates a genotypic structural variation, which not only affects the affinity but also calcium transport efficiency after interaction of CIPK-CBL with calcium exchanger (EcCAX1b) to pull calcium in the vacuole. Based on the expression and in silico study, it can be suggested that by activating EcCAX1b protein, EcCIPK24 plays an important role in high seed Ca2+ accumulation.
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Puranik S, Kam J, Sahu PP, Yadav R, Srivastava RK, Ojulong H, Yadav R. Harnessing Finger Millet to Combat Calcium Deficiency in Humans: Challenges and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1311. [PMID: 28798761 PMCID: PMC5526919 DOI: 10.3389/fpls.2017.01311] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/12/2017] [Indexed: 05/07/2023]
Abstract
Humans require more than 20 mineral elements for healthy body function. Calcium (Ca), one of the essential macromineral, is required in relatively large quantities in the diet for maintaining a sound overall health. Young children, pregnant and nursing women in marginalized and poorest regions of the world, are at highest risk of Ca malnutrition. Elderly population is another group of people most commonly affected by Ca deficiency mainly in the form of osteoporosis and osteopenia. Improved dietary intake of Ca may be the most cost-effective way to meet such deficiencies. Finger millet [Eleusine coracana (L.) Gaertn.], a crop with inherently higher Ca content in its grain, is an excellent candidate for understanding genetic mechanisms associated with Ca accumulation in grain crops. Such knowledge will also contribute toward increasing Ca contents in other staple crops consumed on daily basis using plant-breeding (also known as biofortification) methods. However, developing Ca-biofortified finger millet to reach nutritional acceptability faces various challenges. These include identifying and translating the high grain Ca content to an adequately bioavailable form so as to have a positive impact on Ca malnutrition. In this review, we assess some recent advancements and challenges for enrichment of its Ca value and present possible inter-disciplinary prospects for advancing the actual impact of Ca-biofortified finger millet.
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Affiliation(s)
- Swati Puranik
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Jason Kam
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Pranav P. Sahu
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Rama Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Henry Ojulong
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Rattan Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
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Vinoth A, Ravindhran R. Biofortification in Millets: A Sustainable Approach for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2017; 8:29. [PMID: 28167953 PMCID: PMC5253353 DOI: 10.3389/fpls.2017.00029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 05/04/2023]
Abstract
Nutritional insecurity is a major threat to the world's population that is highly dependent on cereals-based diet, deficient in micronutrients. Next to cereals, millets are the primary sources of energy in the semi-arid tropics and drought-prone regions of Asia and Africa. Millets are nutritionally superior as their grains contain high amount of proteins, essential amino acids, minerals, and vitamins. Biofortification of staple crops is proved to be an economically feasible approach to combat micronutrient malnutrition. HarvestPlus group realized the importance of millet biofortification and released conventionally bred high iron pearl millet in India to tackle iron deficiency. Molecular basis of waxy starch has been identified in foxtail millet, proso millet, and barnyard millet to facilitate their use in infant foods. With close genetic-relatedness to cereals, comparative genomics has helped in deciphering quantitative trait loci and genes linked to protein quality in finger millet. Recently, transgenic expression of zinc transporters resulted in the development of high grain zinc while transcriptomics revealed various calcium sensor genes involved in uptake, translocation, and accumulation of calcium in finger millet. Biofortification in millets is still limited by the presence of antinutrients like phytic acid, polyphenols, and tannins. RNA interference and genome editing tools [zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)] needs to be employed to reduce these antinutrients. In this review paper, we discuss the strategies to accelerate biofortification in millets by summarizing the opportunities and challenges to increase the bioavailability of macro and micronutrients.
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Affiliation(s)
- A Vinoth
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
| | - R Ravindhran
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
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Sharma D, Jamra G, Singh UM, Sood S, Kumar A. Calcium Biofortification: Three Pronged Molecular Approaches for Dissecting Complex Trait of Calcium Nutrition in Finger Millet ( Eleusine coracana) for Devising Strategies of Enrichment of Food Crops. FRONTIERS IN PLANT SCIENCE 2017; 7:2028. [PMID: 28144246 PMCID: PMC5239788 DOI: 10.3389/fpls.2016.02028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 05/07/2023]
Abstract
Calcium is an essential macronutrient for plants and animals and plays an indispensable role in structure and signaling. Low dietary intake of calcium in humans has been epidemiologically linked to various diseases which can have serious health consequences over time. Major staple food-grains are poor source of calcium, however, finger millet [Eleusine coracana (L.) Gaertn.], an orphan crop has an immense potential as a nutritional security crop due to its exceptionally high calcium content. Understanding the existing genetic variation as well as molecular mechanisms underlying the uptake, transport, accumulation of calcium ions (Ca2+) in grains is of utmost importance for development of calcium bio-fortified crops. In this review, we have discussed molecular mechanisms involved in calcium accumulation and transport thoroughly, emphasized the role of molecular breeding, functional genomics and transgenic approaches to understand the intricate mechanism of calcium nutrition in finger millet. The objective is to provide a comprehensive up to date account of molecular mechanisms regulating calcium nutrition and highlight the significance of bio-fortification through identification of potential candidate genes and regulatory elements from finger millet to alleviate calcium malnutrition. Hence, finger millet could be used as a model system for explaining the mechanism of elevated calcium (Ca2+) accumulation in its grains and could pave way for development of nutraceuticals or designer crops.
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Affiliation(s)
- Divya Sharma
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
| | - Gautam Jamra
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
| | - Uma M. Singh
- International Rice Research Institute Division, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Salej Sood
- Indian Council of Agricultural Research-Vivekananda Institute of Hill AgricultureAlmora, India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
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Rajendran HAD, Muthusamy R, Stanislaus AC, Krishnaraj T, Kuppusamy S, Ignacimuthu S, Al-Dhabi NA. Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers. JOURNAL OF CROP SCIENCE AND BIOTECHNOLOGY 2016; 19:275-283. [DOI: 10.1007/s12892-016-0015-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
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Ragupathy S, Dhivya S, Patel K, Sritharan A, Sambandan K, Gartaula H, Sathishkumar R, Khadka K, Nirmala BC, Kumari AN, Newmaster SG. DNA record of some traditional small millet landraces in India and Nepal. 3 Biotech 2016; 6:133. [PMID: 28330205 PMCID: PMC4903100 DOI: 10.1007/s13205-016-0450-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/31/2016] [Indexed: 11/30/2022] Open
Abstract
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK. DNA barcoding employed in this study is proposed as a model for conservation of genetic diversity and an essential step towards documenting and protecting farmers' rights and TK. Our study focuses on 32 landraces of small millets that are still used by indigenous farmers located in the rain fed areas of rural India and Nepal. Traditional knowledge of traits and utility was gathered using participatory methods and semi-structured interviews with key informants. DNA was extracted and sequenced (rbcL, trnH-psbA and ITS2) from 160 samples. Both multivariate analysis of traits and phylogenetic analyses were used to assess diversity among small millet landraces. Our research revealed considerable variation in traits and DNA sequences among the 32 small millet landraces. We utilized a tiered approach using ITS2 DNA barcode to make 100 % accurate landrace (32 landraces) and species (six species) assignments for all 160 blind samples in our study. We have also recorded precious TK of nutritional value, ecological and agricultural traits used by local farmers for each of these traditional landraces. This research demonstrates the potential of DNA barcoding as a reliable identification tool and for use in evaluating and conserving genetic diversity of small millets. We suggest ways in which DNA barcodes could be used in the Protection of Plant Varieties and Farmers' Rights in India and Nepal.
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Affiliation(s)
- Subramanyam Ragupathy
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Shanmughanandhan Dhivya
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Kirit Patel
- International Development Studies Program, Menno Simons College, Canadian Mennonite University, Winnipeg, MB, R3C 0G2, Canada
| | - Abiran Sritharan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Kathirvelu Sambandan
- Post Graduate Department of Plant Science, Avyaiyar Government College for Women, Karaikal, 609 602, U.T. of Puducherry, India
- Centre for Biocultural Diversity, 45A Srinivasan Street, Madipakkam, Chennai, 600091, India
| | - Hom Gartaula
- Department of Anthropology, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Kamal Khadka
- Local Initiatives for Biodiversity, Research and Development (LI-BIRD), P.O. Box 324, Pokhara, Kaski, Nepal
| | - Balasubramanian C Nirmala
- Department of Plant Biology and Plant Biotechnology, S.D.N.B. Vaishnav College for Women, Chromepet, Chennai, Tamil Nadu, 600 044, India
- Centre for Biocultural Diversity, 45A Srinivasan Street, Madipakkam, Chennai, 600091, India
| | - A Nirmala Kumari
- Centre for Excellence in Millets, Tamil Nadu Agricultural University, Atthiyandal, Thiruvannamalai District, Thiruvannamalai, Tamil Nadu, 606 603, India
| | - Steven G Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Kumar A, Metwal M, Kaur S, Gupta AK, Puranik S, Singh S, Singh M, Gupta S, Babu BK, Sood S, Yadav R. Nutraceutical Value of Finger Millet [Eleusine coracana (L.) Gaertn.], and Their Improvement Using Omics Approaches. FRONTIERS IN PLANT SCIENCE 2016; 7:934. [PMID: 27446162 PMCID: PMC4925701 DOI: 10.3389/fpls.2016.00934] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/13/2016] [Indexed: 05/22/2023]
Abstract
The science of nutritional biology has progressed extensively over the last decade to develop food-based nutraceuticals as a form of highly personalized medicine or therapeutic agent. Finger millet [Eleusine coracana (L.) Gaertn.] is a crop with potentially tremendous but under-explored source of nutraceutical properties as compared to other regularly consumed cereals. In the era of growing divide and drawback of nutritional security, these characteristics must be harnessed to develop finger millet as a novel functional food. In addition, introgression of these traits into other staple crops can improve the well-being of the general population on a global scale. The objective of this review is to emphasize the importance of biofortification of finger millet in context of universal health and nutritional crisis. We have specifically highlighted the role that recent biotechnological advancements have to offer for enrichment of its nutritional value and how these developments can commission to the field of nutritional biology by opening new avenues for future research.
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Affiliation(s)
- Anil Kumar
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Mamta Metwal
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Sanveen Kaur
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Atul K. Gupta
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Swati Puranik
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Sadhna Singh
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - B. K. Babu
- ICAR–Vivekananda Institute of Hill AgricultureAlmora, India
| | - Salej Sood
- ICAR–Vivekananda Institute of Hill AgricultureAlmora, India
| | - Rattan Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
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Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, Al-Dhabi NA, Ignacimuthu S. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers. SPRINGERPLUS 2016; 5:120. [PMID: 26900542 PMCID: PMC4749518 DOI: 10.1186/s40064-015-1626-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/16/2015] [Indexed: 12/01/2022]
Abstract
We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60–70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard’s similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard’s similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions.
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Affiliation(s)
- M Ramakrishnan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India
| | - S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Faculty of Biological Sciences, Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT UK
| | - V Duraipandiyan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - N A Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Visiting Professor Program, Deanship of Scientific Research, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
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Singh M, Metwal M, Kumar VA, Kumar A. Identification and molecular characterization of 48 kDa calcium binding protein as calreticulin from finger millet (Eleusine coracana) using peptide mass fingerprinting and transcript profiling. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:672-9. [PMID: 25684084 DOI: 10.1002/jsfa.7139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Attempts were made to identify and characterize the calcium binding proteins (CaBPs) in grain filling stages of finger millet using proteomics, bioinformatics and molecular approaches. RESULTS A distinctly observed blue color band of 48 kDa stained by Stains-all was eluted and analyzed as calreticulin (CRT) using nano liquid chromatography-tandem mass spectrometry (nano LC-MS). Based on the top hits of peptide mass fingerprinting results, conserved primers were designed for isolation of the CRT gene from finger millet using calreticulin sequences of different cereals. The deduced nucleotide sequence analysis of 600 bp amplicon showed up to 91% similarity with CRT gene(s) of rice and other plant species and designated as EcCRT1. Transcript profiling of EcCRT1 showed different levels of relative expression at different stages of developing spikes. The higher expression of EcCRT1 transcripts and protein were observed in later stages of developing spikes which might be due to greater translational synthesis of EcCRT1 protein during seed maturation in finger millet. CONCLUSIONS Preferentially higher synthesis of this CaBP during later stages of grain filling may be responsible for the sequestration of calcium in endoplasmic reticulum of finger millet grains.
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Affiliation(s)
- Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Mamta Metwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Vandana A Kumar
- Department of Biochemistry, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, 63145, Udham Singh Nagar, India
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Sood S, Kumar A, Babu BK, Gaur VS, Pandey D, Kant L, Pattnayak A. Gene Discovery and Advances in Finger Millet [ Eleusine coracana (L.) Gaertn.] Genomics-An Important Nutri-Cereal of Future. FRONTIERS IN PLANT SCIENCE 2016; 7:1634. [PMID: 27881984 PMCID: PMC5101212 DOI: 10.3389/fpls.2016.01634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/17/2016] [Indexed: 05/22/2023]
Abstract
The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2-4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet.
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Affiliation(s)
- Salej Sood
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
- *Correspondence: Salej Sood ;
| | - Anil Kumar
- Molecular Biology and Genetic Engineering, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
- Anil Kumar
| | - B. Kalyana Babu
- Indian Council of Agricultural Research, Indian Institute of Oil Palm ResearchPedavegi, India
| | | | - Dinesh Pandey
- Molecular Biology and Genetic Engineering, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
| | - Lakshmi Kant
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
| | - Arunava Pattnayak
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
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Jain S, Kumar A, Mamidi S, McPhee K. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers. Mol Biotechnol 2014; 56:925-38. [PMID: 24894738 DOI: 10.1007/s12033-014-9772-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.
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Affiliation(s)
- Shalu Jain
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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Mirza N, Taj G, Arora S, Kumar A. Transcriptional expression analysis of genes involved in regulation of calcium translocation and storage in finger millet (Eleusine coracana L. Gartn.). Gene 2014; 550:171-9. [PMID: 25101868 DOI: 10.1016/j.gene.2014.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/31/2014] [Accepted: 08/02/2014] [Indexed: 12/20/2022]
Abstract
Finger millet (Eleusine coracana) variably accumulates calcium in different tissues, due to differential expression of genes involved in uptake, translocation and accumulation of calcium. Ca(2+)/H(+) antiporter (CAX1), two pore channel (TPC1), CaM-stimulated type IIB Ca(2+) ATPase and two CaM dependent protein kinase (CaMK1 and 2) homologs were studied in finger millet. Two genotypes GP-45 and GP-1 (high and low calcium accumulating, respectively) were used to understand the role of these genes in differential calcium accumulation. For most of the genes higher expression was found in the high calcium accumulating genotype. CAX1 was strongly expressed in the late stages of spike development and could be responsible for accumulating high concentrations of calcium in seeds. TPC1 and Ca(2+) ATPase homologs recorded strong expression in the root, stem and developing spike and signify their role in calcium uptake and translocation, respectively. Calmodulin showed strong expression and a similar expression pattern to the type IIB ATPase in the developing spike only and indicating developing spike or even seed specific isoform of CaM affecting the activity of downstream target of calcium transportation. Interestingly, CaMK1 and CaMK2 had expression patterns similar to ATPase and TPC1 in various tissues raising a possibility of their respective regulation via CaM kinase. Expression pattern of 14-3-3 gene was observed to be similar to CAX1 gene in leaf and developing spike inferring a surprising possibility of CAX1 regulation through 14-3-3 protein. Our results provide a molecular insight for explaining the mechanism of calcium accumulation in finger millet.
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Affiliation(s)
- Neelofar Mirza
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G B Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Gohar Taj
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G B Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Sandeep Arora
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G B Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India
| | - Anil Kumar
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G B Pant University of Agriculture & Technology, Pantnagar 263145, Uttarakhand, India.
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Babu BK, Dinesh P, Agrawal PK, Sood S, Chandrashekara C, Bhatt JC, Kumar A. Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs. PLoS One 2014; 9:e99182. [PMID: 24915067 PMCID: PMC4051690 DOI: 10.1371/journal.pone.0099182] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R²) of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R². The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R². Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars.
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Affiliation(s)
- B. Kalyana Babu
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
- Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - Pandey Dinesh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Pawan K. Agrawal
- Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - S. Sood
- Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - C. Chandrashekara
- Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - Jagadish C. Bhatt
- Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
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Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers. Mol Biol Rep 2014; 41:5287-97. [PMID: 24861452 DOI: 10.1007/s11033-014-3400-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
Abstract
Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤ 0.01 and ≤ 0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R (2)) of 10.8%. The QTL for days to 50% flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7% of R (2) respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R(2)-14.1 %) and plant height (P-0.001, R(2)-11.2%). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well adapted germplasm.
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Nirgude M, Babu BK, Shambhavi Y, Singh UM, Upadhyaya HD, Kumar A. Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.). Mol Biol Rep 2014; 41:1189-200. [PMID: 24477581 DOI: 10.1007/s11033-013-2825-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Abstract
Finger millet (Eleusine coracana (L.) Gaertn), holds immense agricultural and economic importance for its high nutraceuticals quality. Finger millets seeds are rich source of calcium and its proteins are good source of essential amino acids. In the present study, we developed 36 EST-SSR primers for the opaque2 modifiers and 20 anchored-SSR primers for calcium transporters and calmodulin for analysis of the genetic diversity of 103 finger millet genotypes for grain protein and calcium contents. Out of the 36 opaque2 modifiers primers, 15 were found polymorphic and were used for the diversity analysis. The highest PIC value was observed with the primer FMO2E33 (0.26), while the lowest was observed FMO2E27 (0.023) with an average value of 0.17. The gene diversity was highest for the primer FMO2E33 (0.33), however it was lowest for FMO2E27 (0.024) at average value of 0.29. The percentage polymorphism shown by opaque2 modifiers primers was 68.23%. The diversity analysis by calcium transporters and calmodulin based anchored SSR loci revealed that the highest PIC was observed with the primer FMCA8 (0.30) and the lowest was observed for FMCA5 (0.023) with an average value of 0.18. The highest gene diversity was observed for primer FMCA8 (0.37), while lowest for FMCA5 (0.024) at an average of 0.21. The opaque2 modifiers specific EST-SSRs could able to differentiate the finger millet genotypes into high, medium and low protein containing genotypes. However, calcium dependent candidate gene based EST-SSRs could broadly differentiate the genotypes based on the calcium content with a few exceptions. A significant negative correlation between calcium and protein content was observed. The present study resulted in identification of highly polymorphic primers (FMO2E30, FMO2E33, FMO2-18 and FMO2-14) based on the parameters such as percentage of polymorphism, PIC values, gene diversity and number of alleles.
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Affiliation(s)
- M Nirgude
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India
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Identification of Anchored Simple Sequence Repeat Markers Associated with Calcium Content in Finger Millet (Eleusine coracana). ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s40011-013-0296-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kumar A, Mirza N, Charan T, Sharma N, Gaur VS. Isolation, characterization and immunolocalization of a seed dominant CaM from finger millet (Eleusine coracana L. Gartn.) for studying its functional role in differential accumulation of calcium in developing grains. Appl Biochem Biotechnol 2014; 172:2955-73. [PMID: 24469585 DOI: 10.1007/s12010-013-0714-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/25/2013] [Indexed: 12/11/2022]
Abstract
To understand the exceptional high grain calcium accumulation in finger millet grains, a calmodulin (CaM) gene that is strongly expressed during developing spikes of high grain calcium genotype was further characterized. Using 5'-3' RACE, the full-length CaM open reading frame (ORF) was isolated and the deduced protein sequence showed the presence of four characteristic EF motifs. Phylogenetic analysis showed that the finger millet CaM (Eleusine coracana calmodulin [EcCaM]) was identical to the rice CaM 1-1. Southern hybridization showed the presence of at least four copies of CaM gene that might be located on different regions of the finger millet "AABB" genome. Immunodetection using monospecific polyclonal anti-EcCaM antibodies revealed that EcCaM is localized in the embryo and aleurone layer and accumulates in higher amounts in high grain calcium genotype compared to the low grain calcium genotype. Furthermore, in silico analysis showed that EcCaM interacts with aquaporin which indicates that calcium is probably delivered to developing spike via mass flow of water. These results indicate that higher expression of CaM might cause greater stimulation of the downstream calcium transport machinery operative in the aleurone layer leading to the higher calcium accumulation in the grains of high grain calcium genotype.
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Affiliation(s)
- Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263 145, India,
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Newmaster SG, Ragupathy S, Dhivya S, Jijo CJ, Sathishkumar R, Patel K. Genomic valorization of the fine scale classification of small millet landraces in southern India. Genome 2013; 56:123-7. [PMID: 23517322 DOI: 10.1139/gen-2012-0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.
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Affiliation(s)
- Steven G Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Goel A, Gaur VS, Arora S, Gupta S, Kumar A. In silico analysis of expression data for identification of genes involved in spatial accumulation of calcium in developing seeds of rice. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:402-13. [PMID: 22734689 DOI: 10.1089/omi.2012.0004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The calcium (Ca(2+)) transporters, like Ca(2+) channels, Ca(2+) ATPases, and Ca(2+) exchangers, are instrumental for signaling and transport. However, the mechanism by which they orchestrate the accumulation of Ca(2+) in grain filling has not yet been investigated. Hence the present study was designed to identify the potential calcium transporter genes that may be responsible for the spatial accumulation of calcium during grain filling. In silico expression analyses were performed to identify Ca(2+) transporters that predominantly express during the different developmental stages of Oryza sativa. A total of 13 unique calcium transporters (7 from massively parallel signature sequencing [MPSS] data analysis, and 9 from microarray analysis) were identified. Analysis of variance (ANOVA) revealed differential expression of the transporters across tissues, and principal component analysis (PCA) exhibited their seed-specific distinctive expression profile. Interestingly, Ca(2+) exchanger genes are highly expressed in the initial stages, whereas some Ca(2+) ATPase genes are highly expressed throughout seed development. Furthermore, analysis of the cis-elements located in the promoter region of the subset of 13 genes suggested that D of proteins play essential roles in regulating the expression of Ca(2+) transporter genes during rice seed development. Based on these results, we developed a hypothetical model explaining the transport and tissue specific distribution of calcium in developing cereal seeds. The model may be extrapolated to understand the mechanism behind the exceptionally high level of calcium accumulation seen in grains like finger millet.
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Affiliation(s)
- Anshita Goel
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
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