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Boussou CK, Das SP, Mohanty M, Das G, Verma DK, Sahoo L, Routray P, Das P. Morphometric and genetic characterization of cultured and wild populations of tilapia, Oreochromis niloticus in India. 3 Biotech 2024; 14:51. [PMID: 38274848 PMCID: PMC10805755 DOI: 10.1007/s13205-023-03895-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
To study genetic variation in Indian populations of tilapia, Oreochromis niloticus, both truss morphometrics and genetic characterization have been performed. In the present study, 88 individuals from two farm populations (GIFT and West Bengal) and one reservoir population (Gujarat) were selected to analyse variations at ten morphometric landmarks and eight microsatellite loci. Truss morphometric analysis showed PCI, PCII, and PCIII expressing 29.1%, 21.36%, and 15.48% of the variance, respectively. Results showed no clear shift in shape between the studied populations of O. niloticus, indicating low morphological variability among them. The number of microsatellite alleles ranged from 3 to 9, while expected heterozygosity (HE) and observed heterozygosity (HO) values ranged from 0.56 (WB) to 0.68 (Guj) and 0.59 (GIFT) to 0.72 (Guj), respectively. The Gujarat and West Bengal populations had the smallest pairwise distance (0.0123) between them, indicating that they were genetically closer. Individuals from GIFT, however, showed the largest distance from the other populations. DNA marker variations revealed the highest genetic variability in the Gujarat population and the lowest variability in the GIFT population. The results of this study will help establish a base population for genetic improvement program and conservation of wild populations.
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Affiliation(s)
| | - Sofia P. Das
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Mausumee Mohanty
- Barcode Biosciences, Dr. Shivaram Karanth Nagar, Bengaluru, 560077 India
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Gargee Das
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Dhananjay K. Verma
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Lakshman Sahoo
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Padmanava Routray
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
| | - Paramananda Das
- Aquaculture production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 India
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Panda S, Swain SK, Sahu BP, Sarangi R. Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers. 3 Biotech 2023; 13:366. [PMID: 37840877 PMCID: PMC10575825 DOI: 10.1007/s13205-023-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Microsatellite markers are being used for molecular identification and characterization as well as estimation of evolution patterns due to their highly polymorphic nature. The repeats hold 40% of the entire genome of Orientia tsutsugamushi (OT), but not yet been characterized. Thus, we investigated the genome-wide presence of microsatellites within nine complete genomes of OT and analyzed their distribution pattern, composition, and complexity. The in-silico study revealed that the genome of OT enriched with microsatellites having a total of 126,187 SSRs and 10,374 cSSRs throughout the genome, of which 70% and 30% are represented within the coding and non-coding regions, respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42-44.43/kb and 6.25-6.59/kb, while for cSSRs this value ranged from 7.06 to 8.1/kb and 0.50 to 0.55/kb, respectively. However, RA and RD were weakly correlated with genome size and incidence of microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). The motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication patterns such as AT-x-AT and CG-x-CG. To our knowledge, this is the first study of microsatellites in the OT genome, where characterization of such variations in repeat sequences would be important in deciphering the origin, rate of mutation, and role of repeat sequences in the genome. More numbers of microsatellites represented within the coding region provide an insight into the genome plasticity that may interfere with gene regulation to mitigate host-pathogen interaction and evolution of the species.
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Affiliation(s)
- Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Subrat Kumar Swain
- Medical Research Laboratory, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Basanta Pravas Sahu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
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Swain SK, Sahu BP, Das SP, Sahoo L, Das PC, Das P. Population genetic structure of fringe-lipped carp, Labeo fimbriatus from the peninsular rivers of India. 3 Biotech 2022; 12:300. [PMID: 36276442 PMCID: PMC9525529 DOI: 10.1007/s13205-022-03369-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Labeo fimbriatus is a medium carp species found throughout India's peninsular river basins and is regarded as a valuable aquaculture resource alongside Indian major carps due to its taste and nutritional value. This species has recently declined dramatically due to habitat degradation and overfishing. Because of its enormous economic importance, a selective breeding programme is likely to be in place to improve performance traits. Knowledge of genetic variation among the base population from which the broodstock will be selected is an important step in this process. A diverse genetic base of broodstock is required to achieve the best response to selection for long-term aquaculture management practices. Consequently, using mitochondrial DNA (ATPase 6 and Control region) and microsatellite markers, we have made the first step toward estimating the level of genetic variation and how it is distributed among the four populations of L. fimbriatus found in peninsular rivers in India. The ATPase 6 gene analysis in four populations revealed 15 haplotypes and 51 variable sites, in contrast to the Control region, which had 60 haplotypes together with 73 variable sites and a haplotype diversity of 0.941. Twelve microsatellite loci displayed estimated allele numbers (N A) ranging from 3 to 19, observed heterozygosity (H O), and expected heterozygosity (H E), respectively, of 0.705 to 0.753 and 0.657 to 0.914. Each marker type showed a significant F ST value, indicating the presence of low to moderate genetic differentiation across entire wild populations. The Godavari, Kaveri, and Mahanadi populations formed one cluster according to the UPGMA, which was based on genetic distance matrix, while the Krishna population formed a separate cluster. The comparative genetic analysis of data from different markers utilized in the current study would enable the identification of the genetic stocks of L. fimbriatus and facilitate conservation measures and selective breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03369-y.
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Affiliation(s)
- Subrat Kumar Swain
- Medical Research Laboratory, IMS and SUM Hospital, SOA University, K8, Kalinga Nagar, Bhubaneswar, India
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Basanta Pravas Sahu
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
- School of Biological Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sofia Priyadarsani Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Pratap Chandra Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
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Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome. Sci Rep 2020; 10:13852. [PMID: 32807836 PMCID: PMC7431841 DOI: 10.1038/s41598-020-70634-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/01/2020] [Indexed: 11/09/2022] Open
Abstract
Genome-wide in-silico identification of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036-1,181 microsatellites per strain. The further screening revealed the presence of 83-107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6-8.4 and 53.0-59.5 bp/kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6-0.8 and 12.1-17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD significantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-significantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)-x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. Finally, in-silico polymorphism was assessed, followed by in-vitro validation using PCR analysis and sequencing. The thirteen polymorphic SSR markers developed in this study were further characterized by mapping with the sequence present in the database. The results of the present study indicate that these SSRs could be a useful tool for identification, analysis of genetic diversity, and understanding the evolutionary status of the virus.
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Hamilton MG, Mekkawy W, Kilian A, Benzie JAH. Single Nucleotide Polymorphisms (SNPs) Reveal Sibship Among Founders of a Bangladeshi Rohu ( Labeo rohita) Breeding Population. Front Genet 2019; 10:597. [PMID: 31275363 PMCID: PMC6593075 DOI: 10.3389/fgene.2019.00597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/05/2019] [Indexed: 01/04/2023] Open
Abstract
Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.
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Affiliation(s)
| | - Wagdy Mekkawy
- WorldFish, Penang, Malaysia
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd., (DArT P/L), University of Canberra, Bruce, ACT, Australia
| | - John A. H. Benzie
- WorldFish, Penang, Malaysia
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
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Behera BK, Baisvar VS, Kunal SP, Meena DK, Panda D, Pakrashi S, Paria P, Das P, Bhakta D, Debnath D, Roy S, Suresh VR, Jena JK. Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:199-205. [PMID: 28024428 DOI: 10.1080/24701394.2016.1267156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The population structure and genetic diversity of Rohu (Labeo rohita Hamilton, 1822) was studied by analysis of the partial sequences of mitochondrial DNA cytochrome b region. We examined 133 samples collected from six locations in three geographically isolated rivers of India. Analysis of 11 haplotypes showed low haplotype diversity (0.00150), nucleotide diversity (π) (0.02884) and low heterogeneity value (0.00374). Analysis of molecular variance (AMOVA) revealed the genetic diversity of L. rohita within population is very high than between the populations. The Fst scores (-0.07479 to 0.07022) were the indication of low genetic structure of L. rohita populations of three rivers of India. Conspicuously, Farakka-Bharuch population pair Fst score of 0.0000, although the sampling sites are from different rivers. The phylogenetic reconstruction of unique haplotypes revealed sharing of a single central haplotype (Hap_1) by all the six populations with a point mutations ranging from 1-25 nucleotides.
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Affiliation(s)
- Bijay Kumar Behera
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Vishwamitra Singh Baisvar
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | | | - Dharmendra Kumar Meena
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Debarata Panda
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Sudip Pakrashi
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Prasenjit Paria
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Pronob Das
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Dibakar Bhakta
- b ICAR-Central Inland Fisheries Research Institute, Regional Center , Guwahati , India
| | - Dipesh Debnath
- b ICAR-Central Inland Fisheries Research Institute, Regional Center , Guwahati , India
| | - Suvra Roy
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - V R Suresh
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - J K Jena
- d Fisheries Division- Indian Council of Agricultural Research , New Delhi , India
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Ullah A, Basak A, Islam MN, Alam MS. Population genetic characterization and family reconstruction in brood bank collections of the Indian major carp Labeo rohita (Cyprinidae:Cypriniformes). SPRINGERPLUS 2015; 4:774. [PMID: 26697284 PMCID: PMC4678141 DOI: 10.1186/s40064-015-1571-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 11/30/2015] [Indexed: 12/02/2022]
Abstract
The founder stock of a captive breeding program is prone to changes in genetic structure due to inbreeding and genetic drift. Genetic characterization of the founder population using suitable molecular markers may help monitor periodic changes in the genetic structure in future. To develop benchmark information about the genetic structure we analyzed six microsatellite loci in the Brodbank collections of rohu (Labeo rohita) originated from three major rivers—the Jamuna, the Padma and the Halda. A total of 28 alleles were detected in 90 individuals with an average of 4.6 alleles per locus. The average observed heterozygosity ranged from 0.655 to 0.705 and the expected heterozygosity ranged from 0.702 to 0.725. The mean FIS values were 0.103, 0.106 and 0.018 for the Jamuna, Padma and Halda fishes respectively. The population pair-wise FST values ranged from 0.0057 to 0.0278. Structure analysis grouped the fishes of the three rivers into two clusters. The numbers of half-sib families were 5, 5 and 4 and the numbers of full-sib families were 12, 10 and 18 for the Halda, Jamuna and the Padma samples respectively. Bottleneck was detected in all the river samples. We recommend to collect more fish from different locations of the major rivers to broaden the genetic variability of the founder stocks of the Brood bank.
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Affiliation(s)
- Ashraf Ullah
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Abhisak Basak
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Md Nazrul Islam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Md Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
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