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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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Balamurugan A, Mallikarjuna MG, Bansal S, Nayaka SC, Rajashekara H, Chellapilla TS, Prakash G. Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection. BMC PLANT BIOLOGY 2024; 24:75. [PMID: 38281915 PMCID: PMC10823742 DOI: 10.1186/s12870-024-04743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.). RESULTS The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains. CONCLUSION The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.
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Affiliation(s)
- Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - S Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore, 570005, India
| | | | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Verbeecke V, Custódio L, Strobbe S, Van Der Straeten D. The role of orphan crops in the transition to nutritional quality-oriented crop improvement. Biotechnol Adv 2023; 68:108242. [PMID: 37640278 DOI: 10.1016/j.biotechadv.2023.108242] [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: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.
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Affiliation(s)
- Vincent Verbeecke
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Laura Custódio
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Rani V, Joshi DC, Joshi P, Singh R, Yadav D. "Millet Models" for harnessing nuclear factor-Y transcription factors to engineer stress tolerance in plants: current knowledge and emerging paradigms. PLANTA 2023; 258:29. [PMID: 37358736 DOI: 10.1007/s00425-023-04186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION The main purpose of this review is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Agriculture faces significant challenges from climate change, bargaining, population, elevated food prices, and compromises with nutritional value. These factors have globally compelled scientists, breeders, and nutritionists to think of some options that can combat the food security crisis and malnutrition. To address these challenges, mainstreaming the climate-resilient and nutritionally unparalleled alternative crops like millet is a key strategy. The C4 photosynthetic pathway and adaptation to low-input marginal agricultural systems make millets a powerhouse of important gene and transcription factor families imparting tolerance to various kinds of biotic and abiotic stresses. Among these, the nuclear factor-Y (NF-Y) is one of the prominent transcription factor families that regulate diverse genes imparting stress tolerance. The primary purpose of this article is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Future cropping systems could be more resilient to climate change and nutritional quality if these practices were implemented.
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Affiliation(s)
- Varsha Rani
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - D C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India
| | - Priyanka Joshi
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, South Carolina, 29634, USA
| | - Rajesh Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
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Bishnoi R, Kaur S, Sandhu JS, Singla D. Genome engineering of disease susceptibility genes for enhancing resistance in plants. Funct Integr Genomics 2023; 23:207. [PMID: 37338599 DOI: 10.1007/s10142-023-01133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
Introgression of disease resistance genes (R-genes) to fight against an array of phytopathogens takes several years using conventional breeding approaches. Pathogens develop mechanism(s) to escape plants immune system by evolving new strains/races, thus making them susceptible to disease. Conversely, disruption of host susceptibility factors (or S-genes) provides opportunities for resistance breeding in crops. S-genes are often exploited by phytopathogens to promote their growth and infection. Therefore, identification and targeting of disease susceptibility genes (S-genes) are gaining more attention for the acquisition of resistance in plants. Genome engineering of S-genes results in targeted, transgene-free gene modification through CRISPR-Cas-mediated technology and has been reported in several agriculturally important crops. In this review, we discuss the defense mechanism in plants against phytopathogens, tug of war between R-genes and S-genes, in silico techniques for identification of host-target (S-) genes and pathogen effector molecule(s), CRISPR-Cas-mediated S-gene engineering, its applications, challenges, and future prospects.
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Affiliation(s)
- Ritika Bishnoi
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Sehgeet Kaur
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Jagdeep Singh Sandhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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Reddy B, Mehta S, Prakash G, Sheoran N, Kumar A. Structured Framework and Genome Analysis of Magnaporthe grisea Inciting Pearl Millet Blast Disease Reveals Versatile Metabolic Pathways, Protein Families, and Virulence Factors. J Fungi (Basel) 2022; 8:jof8060614. [PMID: 35736098 PMCID: PMC9225118 DOI: 10.3390/jof8060614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/10/2022] [Accepted: 05/06/2022] [Indexed: 12/19/2022] Open
Abstract
Magnaporthe grisea (T.T. Herbert) M.E. Barr is a major fungal phytopathogen that causes blast disease in cereals, resulting in economic losses worldwide. An in-depth understanding of the basis of virulence and ecological adaptation of M. grisea is vital for devising effective disease management strategies. Here, we aimed to determine the genomic basis of the pathogenicity and underlying biochemical pathways in Magnaporthe using the genome sequence of a pearl millet-infecting M. grisea PMg_Dl generated by dual NGS techniques, Illumina NextSeq 500 and PacBio RS II. The short and long nucleotide reads could be draft assembled in 341 contigs and showed a genome size of 47.89 Mb with the N50 value of 765.4 Kb. Magnaporthe grisea PMg_Dl showed an average nucleotide identity (ANI) of 86% and 98% with M. oryzae and Pyricularia pennisetigena, respectively. The gene-calling method revealed a total of 10,218 genes and 10,184 protein-coding sequences in the genome of PMg_Dl. InterProScan of predicted protein showed a distinct 3637 protein families and 695 superfamilies in the PMg_Dl genome. In silico virulence analysis revealed the presence of 51VFs and 539 CAZymes in the genome. The genomic regions for the biosynthesis of cellulolytic endo-glucanase and beta-glucosidase, as well as pectinolytic endo-polygalacturonase, pectin-esterase, and pectate-lyases (pectinolytic) were detected. Signaling pathways modulated by MAPK, PI3K-Akt, AMPK, and mTOR were also deciphered. Multicopy sequences suggestive of transposable elements such as Type LTR, LTR/Copia, LTR/Gypsy, DNA/TcMar-Fot1, and Type LINE were recorded. The genomic resource presented here will be of use in the development of molecular marker and diagnosis, population genetics, disease management, and molecular taxonomy, and also provide a genomic reference for ascomycetous genome investigations in the future.
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Affiliation(s)
- Bhaskar Reddy
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
- Correspondence: (B.R.); (A.K.)
| | - Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Ganesan Prakash
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
| | - Neelam Sheoran
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
| | - Aundy Kumar
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
- Correspondence: (B.R.); (A.K.)
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Pendergast TH, Qi P, Odeny DA, Dida MM, Devos KM. A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits. THE PLANT GENOME 2022; 15:e20175. [PMID: 34904374 DOI: 10.1002/tpg2.20175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.
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Affiliation(s)
- Thomas H Pendergast
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Peng Qi
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics-Eastern and Southern Africa, Nairobi, Kenya
| | - Mathews M Dida
- Dep. of Applied Sciences, Maseno Univ., Private Bag-40105, Maseno, Kenya
| | - Katrien M Devos
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
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