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Microsatellite marker development in Spanish mackerel Scomberomorus commerson using third generation sequencing technology.

Authors
  • Joy, Linu1
  • Paulose, Sunitha1
  • Divya, P R2
  • Ravi, Charan1
  • Basheer, V S1
  • Kumar, Rajesh3
  • Singh, Rajeev Kumar3
  • Mohindra, Vindhya3
  • Lal, Kuldeep Kumar3
  • 1 PMFGR Centre, ICAR NBFGR, Kochi, India. , (India)
  • 2 PMFGR Centre, ICAR NBFGR, Kochi, India. [email protected] , (India)
  • 3 ICAR National Bureau of Fish Genetic Resources, Lucknow, India. , (India)
Type
Published Article
Journal
Molecular Biology Reports
Publisher
Springer-Verlag
Publication Date
Dec 01, 2020
Volume
47
Issue
12
Pages
10005–10014
Identifiers
DOI: 10.1007/s11033-020-05975-6
PMID: 33170425
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Spanish mackerel S. commerson belonging to family Scombridae, represent a group of highly commercial marine fisheries with an ever-growing demand world over. Analysing the genetic diversity of this species is of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first multiplex panel set of species-specific microsatellite loci for S. commerson that can be applied when assessing both intra- and inter population genetic variation. Microsatellite marker panels were developed in S. commerson, using Third Generation Sequencing technology in PacBio RSII, based on Single-Molecule Real-Time (SMRT). Thirty- two microsatellite loci were isolated and characterized for S. commerson, by genotyping 20 individuals each obtained from the Kochi and Veraval in the Arabian sea and Chennai along Bay of Bengal coast (n = 3). The number of alleles per locus in S. commerson varied from 4 to 17, while the mean observed and expected heterozygosities ranged from 0.656 to 0.753. The Polymorphic Information Content (PIC) were highly informative, 85% loci with PIC value 0 > 0.75. This suite of markers provides the first species specific nuclear multiplex microsatellite marker panels (32 loci) for S. commerson and thus allows assessment of different populations structures of the species across its distribution range, with more specificity. These newly developed loci have also been validated for cross transferability in another scomberid fish Scomberomorus guttatus.

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