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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Sahoo A, Kar B, Sahoo S, Jena S, Ray A, Padhiari BM, Nayak S. In silico mining of SSR markers from expressed sequence tags of Clematis chinensis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, Sahebi M, Azizi P. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci Rep 2019; 9:3047. [PMID: 30816255 PMCID: PMC6395698 DOI: 10.1038/s41598-019-39944-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/06/2019] [Indexed: 11/24/2022] Open
Abstract
Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - M Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Stefaan P O Werbrouck
- Laboratory of Applied Science In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, University Ghent, Valentin Vaerwyckweg 1, BE-9000, Gent, Belgium
| | - Chee How Teo
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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4
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Interaction of turmeric ( Curcuma longa L.) with beneficial microbes: a review. 3 Biotech 2017; 7:357. [PMID: 29038774 DOI: 10.1007/s13205-017-0971-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022] Open
Abstract
Curcuma longa L., commonly known as turmeric, is a rhizomatous herb of the family Zingiberaceae. It is mostly used as a spice, a coloring agent and broadly used in traditional medicine such as Ayurveda, Unani, etc., Turmeric rhizomes interact with a large numbers of rhizosphere-associated microbial species, and some enter the plant tissue and act as endophytes. Both rhizospheric and endophytic species are directly or indirectly involved in growth promotion and disease management in plants and also play an important role in the modulation of morphological growth, secondary metabolite production, curcumin content, antioxidant properties, etc. The present review focuses on the rhizobacterial and endophytic bacterial and fungal populations associated with the turmeric.
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Awasthi P, Singh A, Sheikh G, Mahajan V, Gupta AP, Gupta S, Bedi YS, Gandhi SG. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:925-931. [PMID: 29158639 PMCID: PMC5671454 DOI: 10.1007/s12298-017-0472-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 07/13/2017] [Accepted: 09/19/2017] [Indexed: 05/11/2023]
Abstract
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.
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Affiliation(s)
- Praveen Awasthi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Ashish Singh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Gulfam Sheikh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Vidushi Mahajan
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Ajai Prakash Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Suphla Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Yashbir S. Bedi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Sumit G. Gandhi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
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EST-SSR marker revealed effective over biochemical and morphological scepticism towards identification of specific turmeric (Curcuma longa L.) cultivars. 3 Biotech 2017; 7:84. [PMID: 28500405 DOI: 10.1007/s13205-017-0701-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/17/2017] [Indexed: 10/19/2022] Open
Abstract
Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern. The polymorphic information content (PIC) of these primers ranged from 0.13 to 0.48. However, only three SSR loci (CSSR 14, CSSR 15, and CSSR 18) gave reproducible unique banding pattern clearly distinguishing the cultivars 'Lakadong' and 'Suvarna' from other cultivars tested. These three unique SSR markers also proved to be effective in identification of 'Lakadong' cultivars when analysed with 88 accessions of turmeric collected from different agro-climatic regions. Furthermore, two identified cultivars (Lakadong and Suvarna) could also be precisely differentiated when analysed and based on phylogenetic tree, with other 94 genotypes of turmeric. The novel SSR markers can be used for identification and authentication of two commercially important turmeric cultivars 'Lakadong' and 'Suvarna'.
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Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Verma S, Singh S, Sharma S, Tewari SK, Roy RK, Goel AK, Rana TS. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:233-42. [PMID: 25964716 PMCID: PMC4411392 DOI: 10.1007/s12298-015-0286-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/21/2015] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.
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Affiliation(s)
- Sushma Verma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shweta Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Suresh Sharma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - S. K. Tewari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - R. K. Roy
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - A. K. Goel
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - T. S. Rana
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
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Chand SK, Nanda S, Rout E, Joshi RK. Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L. Bioinformation 2015; 11:145-50. [PMID: 25987765 PMCID: PMC4421003 DOI: 10.6026/97320630011145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/28/2015] [Indexed: 12/30/2022] Open
Abstract
Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.
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Affiliation(s)
- Subodh Kumar Chand
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Satyabrata Nanda
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Ellojita Rout
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Raj Kumar Joshi
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
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Nguyen TTB, Arimatsu Y, Hong SJ, Brindley PJ, Blair D, Laha T, Sripa B. Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis. Parasitol Res 2015; 114:2263-72. [PMID: 25782682 DOI: 10.1007/s00436-015-4419-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers that have been used for identification and genetic diversity; however, no information about microsatellites of this liver fluke is published so far. We here report microsatellite characterization and marker development for a genetic diversity study in C. sinensis, using a genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (≥12 base pairs) were identified from a genome database of C. sinensis, with hexanucleotide motif being the most abundant (51%) followed by pentanucleotide (18.3%) and trinucleotide (12.7%). The tetranucleotide, dinucleotide, and mononucleotide motifs accounted for 9.75, 7.63, and 0.14%, respectively. The total length of all microsatellites accounts for 0. 72% of 547 Mb of the whole genome size, and the frequency of microsatellites was found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri-, and tetranucleotide, the repeat numbers redundant are six (28%), four (45%), and three (76%), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT, and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and Opisthorchis viverrini. Seven out of 24 loci showed to be heterozygous with observed heterozygosity that ranged from 0.467 to 1. Four primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites, and the genome-wide markers developed may be a useful tool for the genetic study of C. sinensis.
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Affiliation(s)
- Thao T B Nguyen
- WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Laboratory, Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
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Monsalve Fonnegra ZI, Urrea Trujillo AI, Canal Morales A. Organogénesis y embriogénesis en Curcuma longa a partir de capas delgadas de células, segmentos y bases de hoja. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2014. [DOI: 10.15446/rev.colomb.biote.v16n2.40131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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