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Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations

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Abstract

Background

Interspecific hybrids of rohu (Labeo rohita) and catla (Labeo catla) are common, especially in India due to constrained breeding. These hybrids must segregate from their wild parents as part of conservational strategies. This study intended to screen the hybrids from wild rohu and catla parents using both morphometric and molecular approaches.

Methods & Results

The carp samples were collected from Jharkhand and West Bengal, India. The correlation and regression analysis of morphometric features are considered superficial but could be protracted statistically by clustering analysis and further consolidated by nucleotide variations of one mitochondrial and one nuclear gene to differentiate hybrids from their parents. Out of 21 morphometric features, 6 were used for clustering analysis that exhibited discrete separation among rohu, catla, and their hybrids when the data points were plotted in a low-dimensional 2-D plane using the first 2 principal components. Out of 40 selected single nucleotide polymorphism (SNP) positions of the COX1 gene, hybrid showed 100% similarity with catla. Concerning SNP similarity of the 18S rRNA nuclear gene, the hybrid showed 100% similarity with rohu but not with catla; exhibiting its probable parental inheritance.

Conclusions

Along with morphometric analysis, the SNP comparison study together points towards strong evidence of interspecific hybridization between rohu and catla, as these hybrids share both morphological and molecular differences with either parent. However, this study will help screen the hybrids from their wild parents, as a strategy for conservational management.

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Data availability

Generated fish DNA sequences were submitted to GenBank of NCBI and accession numbers were mentioned in the manuscript. A total of 8 DNA sequence accession numbers were mentioned: PP291954, PP291970, PP292005, and PP292006 for COX1 of wild rohu, wild catla, and their 2 hybrids respectively. Another 4 accession numbers were for 18S rRNA DNA sequences like PP296552, PP296554, PP296553, and PP296690 of wild rohu, wild catla, and their 2 hybrids respectively.

References

  1. Hishamunda N, Ridler N, Martone E (2014) Policy and governance in aquaculture: lessons learned and way forward. FAO Fisheries and aquaculture technical paper, p I. 577

  2. Premchand K, Usha Kiranmai G (2017) Study on growth of Indian major carps under different feed treatments in Krishna District Andhrapradesh. Int J Innov Res Creat Technol 2:174–178

    Google Scholar 

  3. Bais B (2018) Fish scenario in India with emphasis on Indian major carps. Int J Avian Wildl Biol 3(6):409–411. https://doi.org/10.15406/ijawb.2018.03.00130

    Article  Google Scholar 

  4. Ullah A, Basak A, Islam MN et al (2015) Population genetic characterization and family reconstruction in brood bank collections of the Indian major carp Labeo rohita (Cyprinidae: Cypriniformes). SpringerPlus 4:774. https://doi.org/10.1186/s40064-015-1571-9

    Article  PubMed  PubMed Central  Google Scholar 

  5. Sahoo L, Mohanty M, Meher PK, Murmu K, Sundaray JK, Das P (2019) Population structure and genetic diversity of hatchery stocks as revealed by combined mtDNA fragment sequences in Indian major carp, Catla catla. Mitochondrial DNA Part A 30(2):289–295

    Article  CAS  Google Scholar 

  6. Sarder MRI, Yeasin M, Jewel MZH, Khan MMR, Simonsen V (2011) Identification of Indian major carps (Catla catla, Labeo rohita and Cirrhinus cirrhosus) and their hybrids by phenotypic traits, allozymes and food habits. Asian Fisheries Sci 24(1):49–61

    Article  Google Scholar 

  7. Allu PKR, Chakraborty B, Das M et al (2014) PCR-based segregation of one hybrid variety of Labeo rohita and Catla catla from their wild types. Aquacult Int 22:775–782. https://doi.org/10.1007/s10499-013-9705-y

    Article  CAS  Google Scholar 

  8. Simonsen V, Hansen M, Sarder M, Alam MS (2004) High level of hybridisation in three species of Indian major carps

  9. Simonsen V, Hansen MM, Mensberg KL, Sarder RI, Alam S (2005) Widespread hybridization among species of Indian major carps in hatcheries, but not in the wild. J Fish Biol 67(3):794–808

    Article  CAS  Google Scholar 

  10. Teletchea F (2009) Molecular identification methods of fish species: reassessment and possible applications. Rev Fish Biol Fisheries 19:265–293. https://doi.org/10.1007/s11160-009-9107-4

    Article  Google Scholar 

  11. Dwivedi AK (2019) Detecting natural hybridization among Indian major carps through advance morphometric approach. BioRxiv, 553941

  12. Laskar BA, Bhattacharjee MJ, Dhar B, Mahadani P, Kundu S et al (2013) The species Dilemma of Northeast Indian Mahseer (Actinopterygii: Cyprinidae): DNA barcoding in clarifying the Riddle. PLoS ONE 8(1):e53704. https://doi.org/10.1371/journal.pone.0053704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhang SM, Reddy PVGK (1991) On the comparative karyomorphology of three Indian major carps, Catla catla (Hamilton), Labeo rohita (Hamilton) and Cirrhinus mrigala (Hamilton) Aquaculture, 97, 7–12

  14. Yoon M, Jung JY, Nam YK, Kim DS (2011) Genetic diversity of thread-sail filefish Stephanolepis cirrhifer populations in Korean coastal waters inferred from mitochondrial DNA sequence analysis. Fisheries Aquat Sci 14(1):16–21

    Article  Google Scholar 

  15. Han HS, Nam BH, Kang JH, Kim YK, Jee YJ, Hur YB, Yoon M (2012) Genetic variation in wild and cultured populations of the sea squirt Halocynthia roretzi inferred from microsatellite DNA analysis. Fisheries Aquat Sci 15(2):151–155

    Article  Google Scholar 

  16. Hong SE, Kim JK, Yu JN, Kim KY, Lee CI, Hong KE, Yoon M (2012) Genetic variation in the Asian shore crab Hemigrapsus sanguineus in Korean coastal waters as inferred from mitochondrial DNA sequences. Fisheries Aquat Sci 15(1):49–56

    Article  CAS  Google Scholar 

  17. Souza-Shibatta L, Kotelok-Diniz T, Ferreira DG, Shibatta OA, Sofia SH, De Assumpcao L, Makrakis MC (2018) Genetic diversity of the endangered neotropical cichlid fish (Gymnogeophagus setequedas) in Brazil. Front Genet 9:325488

    Article  Google Scholar 

  18. Gong J, Zhao R, Deng J, Zhao Y, Zuo J, Huang L, **g M (2018) Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers. Mitochondrial DNA Part A 29(8):1261–1268

    Article  CAS  Google Scholar 

  19. Parveen S, Abbas K, Tayyab M, Hussain M, Naz H, Shafique L (2024) Microsatellite and mtDNA-based exploration of inter-generic hybridization and patterns of genetic diversity in major carps of Punjab, Pakistan. Aquaculture International, pp 1–28

  20. Noorullah M, Zuberi A, Zaman M, Younas W, Hussain S, Kamran M (2023) Assessment of genetic diversity among wild and captive-bred Labeo rohita through microsatellite markers and mitochondrial DNA. Fisheries Aquat Sci 26(12):752–761

    Article  CAS  Google Scholar 

  21. Hamilton MG, Mekkawy W, Benzie JA (2019) Sibship assignment to the founders of a Bangladeshi Catla catla breeding population. Genet Selection Evol 51(1):17

    Article  Google Scholar 

  22. Langille BL, Perry R, Keefe D, Barker O, Marshall HD (2016) Mitochondrial population structure and post-glacial dispersal of longnose sucker Catostomus catostomus in Labrador, Canada: evidence for multiple refugial origins and limited ongoing gene flow. J Fish Biol 89(2):1378–1392

    Article  CAS  PubMed  Google Scholar 

  23. White TJ, Bruns T, Lee SJWT, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: Guide Methods Appl 18(1):315–322

    Google Scholar 

  24. Hatanaka T, Galetti PM (2004) Map** of the 18S and 5S ribosomal RNA genes in the fish Prochilodus argenteus Agassiz, 1829 (Characiformes, Prochilodontidae). Genetica 122:239–244

    Article  CAS  PubMed  Google Scholar 

  25. Sanyal KB, Mukherjee D, Dash G (2018) Isolation and identification of different parasites from Indian major carps and exotic carps from South 24-Parganas, West Bengal. Indian J Anim Sci 88(8):979–984

    Article  CAS  Google Scholar 

  26. Sonowal J, Chetia P, Kardong D (2021) Phylogenetic analysis of Indian freshwater pond mussels Lamellidenscorrianusand L. phenchooganjensis (Bivalvia: Unionidae) from the upper Brahmaputra Basin of Assam, India. Biosci Biotechnol Res Asia 18(1):197

    Article  Google Scholar 

  27. Wu S, **ong J, Yu Y (2015) Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS ONE 10(6):e0131498. https://doi.org/10.1371/journal.pone.0131498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Jayaram KC (1999) The freshwater fishes of Indian region. Narendra Publishing House, Delhi, p 551

    Google Scholar 

  29. Rainboth WJ (1996) FAO species identification field guide for fishery purposes, fishes of the Cambodia Mekong. FAO, Rome, p 265

    Google Scholar 

  30. Taggart JB, Hynes RA, Prodöuhl PA, Ferguson AA (1992) Simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40(6):963–965

    Article  CAS  Google Scholar 

  31. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

    Google Scholar 

  32. Lutz Í, Miranda J, Santana P, Martins T, Ferreira C, Sampaio I, Vallinoto M, Gomes GE (2023) Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction. PLoS ONE 18(2):e0282369. https://doi.org/10.1371/journal.pone.0282369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding of Australia’s fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–1857

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hotelling H (1933) Analysis of a complex of statistical variables into principal components. J Educ Psychol 24:417–441

    Article  Google Scholar 

  35. Ding C, He X (2004) K-means clustering via principal component analysis. In Proceedings of the twenty-first international conference on Machine learning (p. 29)

  36. Bhat N, Ezra BW, Parikesit AA (2019) Use of the DNAChecker Algorithm for improving Bioinformatics Research. Makara J Technol 23(2):Article4. https://doi.org/10.7454/mst.v23i2.3488

    Article  Google Scholar 

  37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  38. Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38(7):3022–3027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Grueber CE (2015) Comparative genomics for biodiversity conservation. Comput Struct Biotechnol J 13:370–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Mastrochirico Filho VA, Freitas MV, Ariede RB, Lira LV, Mendes NJ, Hashimoto DT (2018) Genetic applications in the conservation of neotropical freshwater fish. Biological resources of water. Intechopen, London. 249 – 84

    Google Scholar 

  41. Wong WL, Khoo G (2017) A review of fish taxonomy conventions and species identification techniques. J Surv Fisheries Sci, 54–93

  42. Carro SCS, Louys J, O’Connor S (2018) Shape does matter: a geometric morphometric approach to shape variation in Indo-Pacific fish vertebrae for habitat identification. J Archaeol Sci 99:124–134

    Article  Google Scholar 

  43. Mahfuj MS, Ahmed FF, Hossain MF, Islam SI, Islam MJ, Alam MA, Nadia ZM (2022) Stock structure analysis of the endangered queen Loach,Botia dario (Hamilton 1822) from five Rivers of Northern Bangladesh by using morphometrics:implications for conservation. Fishes 7(1):41

    Article  Google Scholar 

  44. Reddy KP, Varghese TJ (1980) Proc of Indian Acad. Sci (Anim Sci) 89(5):419–429

    Google Scholar 

  45. Cermakova E, Lencova S, Mukherjee S, Horka P, Vobruba S, Demnerova K, Zdenkova K (2023) Identification of Fish species and targeted genetic modifications based on DNA analysis: state of the art. Foods 12(1):228. https://doi.org/10.3390/foods12010228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hulata G (1995) A review of genetic improvement of the common carp (Cyprinus carpio L.) and other cyprinids by crossbreeding, hybridization and selection. Aquaculture 129(1–4):143–155

    Article  Google Scholar 

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Acknowledgements

This work has been supported by Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand by giving working space and providing computer and internet facilities. SG is indebted to Mr. Vineet Vishal for his valuable suggestions on bioinformatics. SG is also thankful to Mr. Vivekananda Mahato for his help in collecting fish samples from Purulia and Ranchi districts. All the authors are indebted to Dr. Surojit Dutta of the GIS department of DSPMU for preparing a GIS map of the areas from where the fish were collected.

Funding

The present work was not supported by any departmental research grant or Government organizations.

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Author notes

  1. Pritam Lenka, Namrata Singh contributed equally to this work.

Authors and Affiliations

  1. Department of Zoology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India

    Pritam Lenka & Namrata Singh

  2. Department of Statistics, Fox School of Business, Temple University, Philadelphia, PA, 19122, USA

    Deepra Ghosh

  3. College of Biotechnology, Birsa Agricultural University, Ranchi, Jharkhand, India

    Pradosh Mahadani

  4. Department of Zoology, Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India

    Sajalendu Ghosh

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Contributions

NS and PL of Dr. Shyama Prasad Mukherjee University were equally involved in making substantial contributions to the design of the work, sample collection, genomic DNA isolation from the same, and interpretation of data. DG of Temple University, USA statistically interpreted, analyzed, and designed the theoretical framework of the manuscript. SG of Dr. Shyama Prasad Mukherjee University drafted the work and with the help of PM from Birsa Agricultural University revised it critically. All authors approved the version of the manuscript to be published and agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Corresponding author

Correspondence to Sajalendu Ghosh.

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This study did not involve either human participants or higher vertebrates or even any living specimens but rather based on dead edible fish sampled from the fish market. So, there is no need for an ethical approval.

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Lenka, P., Singh, N., Ghosh, D. et al. Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations. Mol Biol Rep 51, 738 (2024). https://doi.org/10.1007/s11033-024-09610-6

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