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Kumari N, Mishra GP, Dikshit HK, Gupta S, Roy A, Sinha SK, Mishra DC, Das S, Kumar RR, Nair RM, Aski M. Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean ( Vigna radiata L.) using genotyping-by-sequencing (GBS) approach. PeerJ 2024; 12:e16722. [PMID: 38406271 PMCID: PMC10893866 DOI: 10.7717/peerj.16722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/04/2023] [Indexed: 02/27/2024] Open
Abstract
Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1×Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean.
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Affiliation(s)
- Nikki Kumari
- Genetics, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | | | | | - Soma Gupta
- Genetics, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Anirban Roy
- Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Subodh Kumar Sinha
- Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India
| | - Dwijesh C. Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, Delhi, India
| | - Shouvik Das
- Genetics, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Ranjeet R. Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | | | - Muraleedhar Aski
- Genetics, Indian Agricultural Research Institute, New Delhi, Delhi, India
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Cowden RJ, Markussen B, Ghaley BB, Henriksen CB. The Effects of Light Spectrum and Intensity, Seeding Density, and Fertilization on Biomass, Morphology, and Resource Use Efficiency in Three Species of Brassicaceae Microgreens. PLANTS (BASEL, SWITZERLAND) 2024; 13:124. [PMID: 38202432 PMCID: PMC10780592 DOI: 10.3390/plants13010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Light is a critical component of indoor plant cultivation, as different wavelengths can influence both the physiology and morphology of plants. Furthermore, fertilization and seeding density can also potentially interact with the light recipe to affect production outcomes. However, maximizing production is an ongoing research topic, and it is often divested from resource use efficiencies. In this study, three species of microgreens-kohlrabi; mustard; and radish-were grown under five light recipes; with and without fertilizer; and at two seeding densities. We found that the different light recipes had significant effects on biomass accumulation. More specifically, we found that Far-Red light was significantly positively associated with biomass accumulation, as well as improvements in height, leaf area, and leaf weight. We also found a less strong but positive correlation with increasing amounts of Green light and biomass. Red light was negatively associated with biomass accumulation, and Blue light showed a concave downward response. We found that fertilizer improved biomass by a factor of 1.60 across species and that using a high seeding density was 37% more spatially productive. Overall, we found that it was primarily the main effects that explained microgreen production variation, and there were very few instances of significant interactions between light recipe, fertilization, and seeding density. To contextualize the cost of producing these microgreens, we also measured resource use efficiencies and found that the cheaper 24-volt LEDs at a high seeding density with fertilizer were the most efficient production environment for biomass. Therefore, this study has shown that, even with a short growing period of only four days, there was a significant influence of light recipe, fertilization, and seeding density that can change morphology, biomass accumulation, and resource input costs.
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Affiliation(s)
- Reed John Cowden
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 30, 2630 Taastrup, Denmark; (B.B.G.); (C.B.H.)
| | - Bo Markussen
- Department of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark;
| | - Bhim Bahadur Ghaley
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 30, 2630 Taastrup, Denmark; (B.B.G.); (C.B.H.)
| | - Christian Bugge Henriksen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 30, 2630 Taastrup, Denmark; (B.B.G.); (C.B.H.)
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Dutta H, K. M. S, Aski MS, Mishra GP, Sinha SK, Vijay D, C. T. MP, Das S, Pawar PAM, Mishra DC, Singh AK, Kumar A, Tripathi K, Kumar RR, Gupta S, Kumar S, Dikshit HK. Morpho-biochemical characterization of a RIL population for seed parameters and identification of candidate genes regulating seed size trait in lentil ( Lens culinaris Medik.). FRONTIERS IN PLANT SCIENCE 2023; 14:1091432. [PMID: 36875597 PMCID: PMC9975752 DOI: 10.3389/fpls.2023.1091432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The seed size and shape in lentil (Lens culinaris Medik.) are important quality traits as these influences the milled grain yield, cooking time, and market class of the grains. Linkage analysis was done for seed size in a RIL (F5:6) population derived by crossing L830 (20.9 g/1000 seeds) with L4602 (42.13 g/1000 seeds) which consisted of 188 lines (15.0 to 40.5 g/1000 seeds). Parental polymorphism survey using 394 SSRs identified 31 polymorphic primers, which were used for the bulked segregant analysis (BSA). Marker PBALC449 differentiated the parents and small seed size bulk only, whereas large seeded bulk or the individual plants constituting the large-seeded bulk could not be differentiated. Single plant analysis identified only six recombinant and 13 heterozygotes, of 93 small-seeded RILs (<24.0 g/1000 seed). This clearly showed that the small seed size trait is very strongly regulated by the locus near PBLAC449; whereas, large seed size trait seems governed by more than one locus. The PCR amplified products from the PBLAC449 marker (149bp from L4602 and 131bp from L830) were cloned, sequenced and BLAST searched using the lentil reference genome and was found amplified from chromosome 03. Afterward, the nearby region on chromosome 3 was searched, and a few candidate genes like ubiquitin carboxyl-terminal hydrolase, E3 ubiquitin ligase, TIFY-like protein, and hexosyltransferase having a role in seed size determination were identified. Validation study in another RIL mapping population which is differing for seed size, showed a number of SNPs and InDels among these genes when studied using whole genome resequencing (WGRS) approach. Biochemical parameters like cellulose, lignin, and xylose content showed no significant differences between parents and the extreme RILs, at maturity. Various seed morphological traits like area, length, width, compactness, volume, perimeter, etc., when measured using VideometerLab 4.0 showed significant differences for the parents and RILs. The results have ultimately helped in better understanding the region regulating the seed size trait in genomically less explored crops like lentils.
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Affiliation(s)
- Haragopal Dutta
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Shivaprasad K. M.
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar S. Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Gyan P. Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Dunna Vijay
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Manjunath Prasad C. T.
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Shouvik Das
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, Faridabad, India
| | | | - Dwijesh C. Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Sanjeev Gupta
- Krishi Bhawan, Indian Council of Agricultural Research, New Delhi, India
| | - Shiv Kumar
- South Asia and China Program, International Center for Agricultural Research in the Dry Areas, National Agriculture Science Complex (NASC) Complex, New Delhi, India
| | - Harsh Kumar Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
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Gupta A, Sharma T, Singh SP, Bhardwaj A, Srivastava D, Kumar R. Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security. Front Genet 2023; 14:1053810. [PMID: 36760994 PMCID: PMC9905132 DOI: 10.3389/fgene.2023.1053810] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered "living superfood/functional food" due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens'stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.
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Affiliation(s)
- Astha Gupta
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, India,*Correspondence: Astha Gupta, ; Rajendra Kumar,
| | - Tripti Sharma
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University,, Kanpur, India
| | - Archana Bhardwaj
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India
| | - Deepti Srivastava
- Department of Agriculture, Integral Institute of Agricultural Science and Technology, Integral University, Lucknow, Uttar Pradesh, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Astha Gupta, ; Rajendra Kumar,
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Dutta H, Mishra GP, Aski MS, Bosamia TC, Mishra DC, Bhati J, Sinha SK, Vijay D, C. T. MP, Das S, Pawar PAM, Kumar A, Tripathi K, Kumar RR, Yadava DK, Kumar S, Dikshit HK. Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.). Front Genet 2022; 13:942079. [PMID: 36035144 PMCID: PMC9399355 DOI: 10.3389/fgene.2022.942079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Market class, cooking time, quality, and milled grain yield are largely influenced by the seed size and shape of the lentil (Lens culinaris Medik.); thus, they are considered to be important quality traits. To unfold the pathways regulating seed size in lentils, a transcriptomic approach was performed using large-seeded (L4602) and small-seeded (L830) genotypes. The study has generated nearly 375 million high-quality reads, of which 98.70% were properly aligned to the reference genome. Among biological replicates, very high similarity in fragments per kilobase of exon per million mapped fragments values (R > 0.9) showed the consistency of RNA-seq results. Various differentially expressed genes associated mainly with the hormone signaling and cell division pathways, transcription factors, kinases, etc. were identified as having a role in cell expansion and seed growth. A total of 106,996 unigenes were used for differential expression (DE) analysis. String analysis identified various modules having certain key proteins like Ser/Thr protein kinase, seed storage protein, DNA-binding protein, microtubule-associated protein, etc. In addition, some growth and cell division–related micro-RNAs like miR3457 (cell wall formation), miR1440 (cell proliferation and cell cycles), and miR1533 (biosynthesis of plant hormones) were identified as having a role in seed size determination. Using RNA-seq data, 5254 EST-SSR primers were generated as a source for future studies aiming for the identification of linked markers. In silico validation using Genevestigator® was done for the Ser/Thr protein kinase, ethylene response factor, and Myb transcription factor genes. It is of interest that the xyloglucan endotransglucosylase gene was found differentially regulated, suggesting their role during seed development; however, at maturity, no significant differences were recorded for various cell wall parameters including cellulose, lignin, and xylose content. This is the first report on lentils that has unfolded the key seed size regulating pathways and unveiled a theoretical way for the development of lentil genotypes having customized seed sizes.
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Affiliation(s)
- Haragopal Dutta
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Gyan P. Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
| | - Muraleedhar S. Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Tejas C. Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Dwijesh C. Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jyotika Bhati
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dunna Vijay
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Manjunath Prasad C. T.
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Shouvik Das
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, Faridabad, India
| | | | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- South Asia and China Program, International Center for Agricultural Research in the Dry Areas, NASC Complex, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
| | - Harsh Kumar Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Gyan P. Mishra, ; Shiv Kumar, ; Harsh Kumar Dikshit,
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