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Malik G, Dhatt AS, Malik AA. A Review of Genetic Understanding and Amelioration of Edible Allium Species. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2019.1709202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Geetika Malik
- Division of Vegetable Science and Floriculture, ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K, India
| | - Ajmer Singh Dhatt
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ajaz Ahmed Malik
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar, J&K, India
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Khandagale K, Krishna R, Roylawar P, Ade AB, Benke A, Shinde B, Singh M, Gawande SJ, Rai A. Omics approaches in Allium research: Progress and way ahead. PeerJ 2020; 8:e9824. [PMID: 32974094 PMCID: PMC7486827 DOI: 10.7717/peerj.9824] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. METHOD In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. RESULTS Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. CONCLUSION All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.
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Affiliation(s)
- Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Praveen Roylawar
- Department of Botany, S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Avinash B. Ade
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ashwini Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Bharat Shinde
- Vidya Pratishthans’s Arts Science and commerce college, Baramati, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | | | - Ashutosh Rai
- Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
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Barboza K, Beretta V, Kozub PC, Salinas C, Morgenfeld MM, Galmarini CR, Cavagnaro PF. Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Mol Genet Genomics 2018; 293:1091-1106. [PMID: 29705936 DOI: 10.1007/s00438-018-1442-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/25/2018] [Indexed: 02/04/2023]
Abstract
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2-5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium.
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Affiliation(s)
- Karina Barboza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Vanesa Beretta
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Perla C Kozub
- Facultad de Ciencias Agrarias (FCA), Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Cecilia Salinas
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
| | - Mauro M Morgenfeld
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Claudio R Galmarini
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
- Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Pablo F Cavagnaro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina.
- Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina.
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Gil J, Um Y, Kim S, Kim OT, Koo SC, Reddy CS, Kim SC, Hong CP, Park SG, Kim HB, Lee DH, Jeong BH, Chung JW, Lee Y. Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing. Genes (Basel) 2017; 8:E238. [PMID: 28934115 PMCID: PMC5664088 DOI: 10.3390/genes8100238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.
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Affiliation(s)
- Jinsu Gil
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Yurry Um
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Korea.
| | - Serim Kim
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Ok Tae Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Sung Cheol Koo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Chinreddy Subramanyam Reddy
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea.
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju 63240, Korea.
| | | | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Ho Bang Kim
- Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea.
| | - Dong Hoon Lee
- Department of Biosystems Engineering, Chungbuk National University, Chungju 28644, Korea.
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
| | - Yi Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
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