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Gowd TYM, Deo C, Manjunathagowda DC, Mahajan V, Dutta R, Bhutia ND, Singh B, Mounika V. Deciphering genetic diversity phylogeny and assembly of Allium species through micro satellite markers on nuclear DNA. Heliyon 2024; 10:e31650. [PMID: 38845887 PMCID: PMC11153109 DOI: 10.1016/j.heliyon.2024.e31650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
The genus Allium is the most diverse, with cultivated crops such as onion, garlic, bunching onion, chives, leeks, and shallots, and several wild and semi-domesticated Allium species utilized as minor vegetables. These minor species are the genetic resources for various abiotic and biotic stresses. To employ underutilized species in breeding programmes, the magnitude of the genetic background of cultivated and semi-domesticated alliums, the phylogeny and diversity of the population must be known. In this study, nineteen SSR markers were employed to study the divergence and population structure of 95 Allium accessions which includes species, varieties, and interspecific hybrids, yielded 92 polymorphic loci, averaging 4.84 loci per SSR. PIC values range between 0.24 (ACM 018) and 0.98 (ACM 099). The cross transferability of ACM markers among Allium species ranges from 1.33 to 10.53 per cent, which is relatively low. The genotypes investigated were clustered into four primary clusters A, B, C, and D with 13 sub clusters I-XIII, conferring to the clustering results. The population structure investigations also found that K is a peak at value 4, implying that the population is predominantly segregated into four distinct groups, which associates the clustering pattern. The employed SSR markers adeptly unravel the complexities of diversity within alliums, holding promise for refining future breeding programs targeting elite progenies.
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Affiliation(s)
- Talamarla Yeswanth Mahidar Gowd
- Department of Vegetable Science, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, India
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India
| | - Chandra Deo
- Department of Vegetable Science, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, India
| | - Dalasanuru Chandregowda Manjunathagowda
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Hessaraghatta, Bengaluru, Karnataka, India
| | - Vijay Mahajan
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India
| | - Ram Dutta
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India
| | - Nangsol Dolma Bhutia
- Department of Vegetable Science, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, India
| | - Barun Singh
- Department of Fruit Science, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, India
| | - Vadde Mounika
- Department of Vegetable Science, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, India
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Jiang Y, Li Z, Yue R, Liu G, Yang M, Long C, Yan D. Evidential support for garlic supplements against diabetic kidney disease: a preclinical meta-analysis and systematic review. Food Funct 2024; 15:12-36. [PMID: 38051214 DOI: 10.1039/d3fo02407e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Garlic (Allium sativum L.) is a popular spice that is widely used for food and medicinal purposes and has shown potential effects on diabetic kidney disease (DKD). Nevertheless, systematic preclinical studies are still lacking. In this meta-analysis and systematic review, we evaluated the role and potential mechanisms of action of garlic and its derived components in animal models of DKD. We searched eight databases for relevant studies from the establishment of the databases to December 2022 and updated in April 2023 before the completion of this review. A total of 24 trials were included in the meta-analysis. It provided preliminary evidence that supplementing with garlic could improve the indicators of renal function (BUN, Scr, 24 h urine volume, proteinuria, and KI) and metabolic disorders (BG, insulin, and body weight). Meanwhile, the beneficial effects of garlic and its components in DKD could be related to alleviating oxidative stress, suppressing inflammatory reactions, delaying renal fibrosis, and improving glucose metabolism. Furthermore, time-dose interval analysis exhibited relatively greater effectiveness when garlic products were supplied at doses of 500 mg kg-1 with interventions lasting 8-10 weeks, and garlic components were administered at doses of 45-150 mg kg-1 with interventions lasting 4-10 weeks. This meta-analysis and systematic review highlights for the first time the therapeutic potential of garlic supplementation in animal models of DKD and offers a more thorough evaluation of its effects and mechanisms to establish an evidence-based basis for designing future clinical trials.
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Affiliation(s)
- Yayi Jiang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Zihan Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Rensong Yue
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Guojie Liu
- School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Maoyi Yang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Caiyi Long
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| | - Dawei Yan
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
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Shamshad S, Rizvi KA, Shehnaz H, Jatoi SA, Shahnaz L, Naqvi SMS, Qasim M, Zainab T, Haider A. Novel NARC-G1 garlic: comparative allicin quantification with morpho-biochemical & genetic profiling. BRAZ J BIOL 2024; 84:e262697. [DOI: 10.1590/1519-6984.262697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Garlic (Allium sativum) is an important cash food crop, and the biotechnology industry has considerable interest in the plant because of its medicinal importance. These medicinal properties are attributed to organosulphur compounds as the accumulation of these compounds varies according to genotype, locality, light quality, and cultivation practices. In this study, we compared a newly developed garlic variety NARC-G1 by National Agricultural Research Centre (NARC), Islamabad, Pakistan with three different garlic cultivars and highlighted the distinctive attributes like phenotypic characteristics, the content of allicin, elemental profile, and gene polymorphism. Phenotypic analysis showed NARC-G1 has significantly higher bulb weight (66.36g ± 18.58), single clove weight (5.87g ± 1.041), and clove width (17.41mm ± 0.95) which directly correlates to the size of the garlic. The analytical analysis showed the highest allicin content (4.82 ± 0.001) in NARC-G1. Genotyping of the alliinase in all four cultivars showed indels in the gene resulting in distinguishable changes in organosulphur compounds’ profile. NARC-G1 is unique from other garlic cultivars and could be the best choice for mass production with proper cultivation and irrigation management. Moreover, for Pakistan NARC-G1 could be a potential contender to earn the industrial benefits with inland cultivation instead of importing garlic alleviating the economic burden.
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Affiliation(s)
- S. Shamshad
- Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - K. A. Rizvi
- Pir Mehr Ali Shah Arid Agriculture University Rawalpindi,, Pakistan
| | - H. Shehnaz
- Sindh Madressatul Islam University, Pakistan
| | - S. A. Jatoi
- National Agriculture Research Center, Pakistan
| | | | | | - M. Qasim
- Hydrocarbon Development Institute of Pakistan, Pakistan
| | - T. Zainab
- Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Pakistan; Pir Mehr Ali Shah Arid Agriculture University Rawalpindi,, Pakistan
| | - A. Haider
- Chemico Bacteriological Laboratory, Pakistan
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Tan C, Zhang H, Chen H, Guan M, Zhu Z, Cao X, Ge X, Zhu B, Chen D. First Report on Development of Genome-Wide Microsatellite Markers for Stock ( Matthiola incana L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:748. [PMID: 36840095 PMCID: PMC9965543 DOI: 10.3390/plants12040748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.
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Affiliation(s)
- Chen Tan
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Haimei Zhang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Haidong Chen
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Miaotian Guan
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Zhenzhi Zhu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Xueying Cao
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Xianhong Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 431700, China
| | - Bo Zhu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Daozong Chen
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
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Moradi M, Khaleghi A, Khadivi A. Morphological variability of wild-growing crown imperial (Fritillaria imperialis L.) germplasm in central region of Iran-implications for in-situ conservation initiatives. BMC PLANT BIOLOGY 2023; 23:12. [PMID: 36604620 PMCID: PMC9817337 DOI: 10.1186/s12870-022-04032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Crown imperial (Fritillaria imperialis L.) is a threatened bulbous plant which has great ornamental and medicinal values and importance. In the present study, a total of 100 specimens of wild-growing F. imperialis from 10 natural areas of Markazi province, Iran, representing one of the main centers of genetic diversity of this species, were evaluated using 37 phenotypic attributes during April 2021. RESULTS High level of genetic variation within populations (75%) and low levels of genetic variation among populations (25%) was revealed. The highest coefficient of variation (CV) was found in leaf trichome (82.00%) and then margin of crown leaves (80.44%). In addition, flower color (CV = 50.86%), flower number (CV = 44.61%), peduncle diameter (CV = 33.44%), and plant length (CV = 32.55%)-all important from an ornamental point of view- showed relatively high CV values. The CV was the lowest for flower shape, filament color, bulb shape, bulblet number, and floral scent. Ward cluster analysis identified two main clusters, containing 14 and 86 specimens, respectively. The first group consisted mainly of specimens from the adjacent Shahbaz and Rasvand populations. According to the principal component analysis (PCA), the first six components of data accounted for 88.36% of total variance. The Shahbaz-1, Shahbaz-2, Shahbaz-6, Shahbaz-7, Shahbaz-9, and Bolagh-8 specimens showed the highest variation and were separated from others, which they can be used further in breeding programs, while Sarchal-2, Bolagh-3, and Chepeqli-4 specimens showed the lowest variability. Moreover, the studied populations were clustered into four distinct groups, each including populations that were geographically close to one another. CONCLUSIONS Although the examined specimens revealed high genetic diversity herein, the results indicated that wild-growing populations of F. imperialis are still at risk suffering from overcollection in the most of studied areas, especially in Deh-Sad and Tureh.
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Affiliation(s)
- Mohammad Moradi
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran
| | - Alireza Khaleghi
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran.
| | - Ali Khadivi
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran.
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Tang W, Lin J, Wang Y, An H, Chen H, Pan G, Zhang S, Guo B, Yu K, Li H, Fang X, Zhang Y. Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:48. [PMID: 36152074 PMCID: PMC9509510 DOI: 10.1186/s12284-022-00594-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown. RESULTS Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others. CONCLUSIONS Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.
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Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Yanping Wang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Hongzhou An
- The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, People's Republic of China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Baowei Guo
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, People's Republic of China
| | - Kun Yu
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Huayong Li
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China.
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Brahimi A, Landschoot S, Bekaert B, Hajji L, Hajjaj H, Audenaert K, Haesaert G, Mazouz H. Exploring the genetic and phenotypic diversity within and between onion (Allium cepa L.) ecotypes in Morocco. J Genet Eng Biotechnol 2022; 20:96. [PMID: 35780465 PMCID: PMC9250909 DOI: 10.1186/s43141-022-00381-w] [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: 03/29/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022]
Abstract
Background Gaining insight into crop diversity, both at the genetic and phenotypic levels, is of prime importance for onion breeding with an enhanced yield and quality in combination with improved resistance to biotic and abiotic stresses. In the current study, 192 different onion plants, representing 16 ecotypes, were characterized using ISSR markers. Results Based on the ISSR marker profile, there was a clear grouping of the plants into 16 different ecotypes. Though the 16 populations originated from the same geographic region in Morocco, a significant genetic diversity was detected. After a genomic characterization, field trials in three different environments in Morocco were laid out. The phenotypic characterization showed that there were always significant differences between ecotypes, and for most traits, there was also a significant environmental effect and a significant interaction between environment and ecotype. The broad-sense heritability (H2) for the phenotypic traits associated with color (L*, a*, and b*) was the largest (84.2%, 80.6%, 79.2%), demonstrating that color is conditioned primarily by genetic factors. In contrast, the H2 for yield was the lowest (41.8%), indicating that the environment has a substantial effect on yield. In addition, there was a significant association between the presence/absence of certain bands and various phenotypic traits. Conclusion ISSR markers are a powerful tool in distinguishing onion ecotypes. In addition, significant associations between marker scores and phenotypic traits could be detected, representing particular importance for future breeding programs.
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Affiliation(s)
- Amal Brahimi
- Biotechnologies and Valorization of Biological Resources Laboratory, Faculty of Science of Meknes, University of Moulay Ismail, P.B 11201, Zitoune, Meknes, Morocco.
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Lhoussain Hajji
- Biotechnologies and Valorization of Biological Resources Laboratory, Faculty of Science of Meknes, University of Moulay Ismail, P.B 11201, Zitoune, Meknes, Morocco
| | - Hassan Hajjaj
- Biotechnologies and Valorization of Biological Resources Laboratory, Faculty of Science of Meknes, University of Moulay Ismail, P.B 11201, Zitoune, Meknes, Morocco
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Hamid Mazouz
- Biotechnologies and Valorization of Biological Resources Laboratory, Faculty of Science of Meknes, University of Moulay Ismail, P.B 11201, Zitoune, Meknes, Morocco
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Benke AP, Krishna R, Mahajan V, Ansari WA, Gupta AJ, Khar A, Shelke P, Thangasamy A, Shabeer TPA, Singh M, Bhagat KP, Manjunathagowda DC. Genetic diversity of Indian garlic core germplasm using agro-biochemical traits and SRAP markers. Saudi J Biol Sci 2021; 28:4833-4844. [PMID: 34354473 PMCID: PMC8324993 DOI: 10.1016/j.sjbs.2021.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/23/2022] Open
Abstract
The characterization of garlic germplasm improves its utility, despite the fact that garlic hasn't been used much in the past. Garlic has an untapped genetic pool of immense economic and medicinal value in India. Hence, using heuristic core collection approach, a core set of 46 accessions were selected from 625 Indian garlic accessions based on 13 quantitative and five qualitative traits. The statistical measures (CV per cent, CR per cent, VR per cent) were used to sort the core set using Shannon-Wiener diversity index and the Nei diversity index. In addition, the variation within the core set was tested for 18 agro-morphological and six biochemical characteristics (allicin, phenol content, pyruvic acid, protein, allyl methyl thiosulfinate (AMTHS), and methyl allyl thiosulfinate (MATHS)). Further study of the core set's molecular diversity was performed using sequence related amplified polymorphism (SRAP) markers, which revealed a wide range of diversity among the core set's accessions, with an average polymorphism efficiency (PE) of 80.59 percent, polymorphism information content (PIC) of 0.29, effective multiplex ratio (EMR) of 3.51, and marker index (MI) of 0.99. The findings of this study will be useful in identifying high-yielding, elite garlic germplasm lines with the trait of interest. Since this core set is indicative of total germplasm, these selected breeding lines will be used for genetic improvement of garlic in the future.
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Affiliation(s)
- Ashwini Prashant Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Vijay Mahajan
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Waquar Akhter Ansari
- Department of Botany, Savitribai Phule Pune University, Pune 41100, Maharashtra, India
| | - Amar Jeet Gupta
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Anil Khar
- Department of Vegetable Science, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Poonam Shelke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - A. Thangasamy
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | | | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar–410505, Pune, Maharashtra, India
| | - Kiran P. Bhagat
- ICAR-Directorate of Floriculture, Pune 411005, Maharashtra, India
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Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Sci Rep 2020; 10:15312. [PMID: 32943659 PMCID: PMC7498607 DOI: 10.1038/s41598-020-71984-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
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Affiliation(s)
- Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - Jaypal N Darbar
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Mita Bagchi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. .,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.
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Zhang J, Yan J, Huang S, Pan G, Chang L, Li J, Zhang C, Tang H, Chen A, Peng D, Biswas A, Zhang C, Zhao L, Li D. Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers. Front Genet 2020; 11:958. [PMID: 33061939 PMCID: PMC7518120 DOI: 10.3389/fgene.2020.00958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.
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Affiliation(s)
- Jiangjiang Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jiangtao Yan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siqi Huang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Gen Pan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Li Chang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jianjun Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Chao Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huijuan Tang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Anguo Chen
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ashok Biswas
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Cuiping Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Lining Zhao
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Defang Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
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Liu H, Wen Y, Cui M, Qi X, Deng R, Gao J, Cheng Z. Histological, Physiological and Transcriptomic Analysis Reveal Gibberellin-Induced Axillary Meristem Formation in Garlic ( Allium sativum). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9080970. [PMID: 32751960 PMCID: PMC7464525 DOI: 10.3390/plants9080970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 05/11/2023]
Abstract
The number of cloves in a garlic bulb is controlled by axillary meristem differentiation, which directly determines the propagation efficiency. Our previous study showed that injecting garlic plants with gibberellins (GA3) solution significantly increased clove number per bulb. However, the physiological and molecular mechanism of GA-induced axillary bud formation is still unknown. Herein, dynamic changes in histology, phytohormones, sugars and related genes expression at 2, 4, 8, 16 and 32 days after treatment (DAT) were investigated. Histological results indicated two stages (axillary meristem initiation and dormancy) were in the period of 0-30 days after GA3 treatment. Application of GA3 caused a significant increase of GA3 and GA4, and the downregulation of AsGA20ox expression. Furthermore, the change trends in zeatin riboside (ZR) and soluble sugar were the same, in which a high level of ZR at 2 DAT and high content of soluble sugar, glucose and fructose at 4 DAT were recorded, and a low level of ZR and soluble sugar arose at 16 and 32 DAT. Overall, injection of GA3 firstly caused the downregulation of AsGA20ox, a significant increase in the level of ZR and abscisic acid (ABA), and the upregulation of AsCYP735 and AsAHK to activate axillary meristem initiation. Low level of ZR and soluble sugar and a high level of sucrose maintained axillary meristem dormancy.
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Fu L, Ding Z, Kumpeangkeaw A, Tan D, Han B, Sun X, Zhang J. De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:133-142. [PMID: 32158126 PMCID: PMC7036385 DOI: 10.1007/s12298-019-00726-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/11/2019] [Accepted: 10/18/2019] [Indexed: 05/12/2023]
Abstract
Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Wuhan, 430070 China
- Department of Agriculture, Song Khla Agricultural Research and Development Center, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla 90110 Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
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Liu W, Xu Y, Li Z, Fan J, Yang Y. Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra). Mol Biol Rep 2019; 46:6087-6098. [PMID: 31502192 DOI: 10.1007/s11033-019-05044-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022]
Abstract
The complete genome sequence provides the opportunity for genome-wide and coding region analysis of SSRs in the king cobra and for cross-species identification of microsatellite markers in the Chinese cobra. In the Ophiophagus hannah genome, tetranucleotide repeats (38.03%) were the most abundant category, followed by dinucleotides (23.03%), pentanucleotides (13.07%), mononucleotides (11.78%), trinucleotides (11.49%) and hexanucleotides (2.6%). Twenty predominant motifs in the O. hannah genome were (A)n (C)n, (AC)n, (AG)n, (AT)n, (AGG)n, (AAT)n, (AAG)n, (AAC)n, (ATG)n, (ATAG)n, (AAGG)n, (ATCT)n, (CCTT)n, (ATTT)n, (AAAT)n, (AATAG)n, (ATTCT)n, (ATATGT)n, (AGATAT)n. In total, 4344 SSRs were found in coding sequences (CDSs). Tetranucleotides (52.79%) were the most abundant microsatellite type in CDS, followed by trinucleotides (28.50%), dinucleotides (11.02%), pentanucleotides (4.42%), mononucleotides (1.77%), and hexanucleotides (1.50%). A total of 984 CDSs containing microsatellites were assigned 11152 Gene Ontology (GO) functional terms. Gene Ontology (GO) analysis demonstrated that cellular process, cell and binding were the most frequent GO terms in biological process, cellular component and molecular function, respectively. Thirty-two novel highly polymorphic (PIC > 0.5) SSR markers for Naja atra were developed from cross-species amplification based on the tetranucleotide microsatellite sequences in the king cobra genome. The number of alleles (NA) per locus had between 3 and 11 alleles with an average of 6.5, the polymorphism information content (PIC) value ranged from 0.521 to 0.858 (average = 0.707), the observed heterozygosity (Ho) of 32 microsatellite loci ranged from 0.292 to 0.875 (mean = 0.678), the expected heterozygosity (HE) ranged from 0.561 to 0.889 (average = 0.761), and 3 microsatellite loci exhibited statistically significant departure from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.003).
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Affiliation(s)
- Wencong Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Yongtao Xu
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zekun Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Jun Fan
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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