Microsatellite marker development in Spanish mackerel Scomberomorus commerson using third generation sequencing technolo
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Microsatellite marker development in Spanish mackerel Scomberomorus commerson using third generation sequencing technology Linu Joy1 · Sunitha Paulose1 · PR Divya1 · Charan Ravi1 · VS Basheer1 · Rajesh Kumar2 · Rajeev Kumar Singh2 · Vindhya Mohindra2 · Kuldeep Kumar Lal2 Received: 21 May 2020 / Accepted: 3 November 2020 © Springer Nature B.V. 2020
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. Keywords Spanish mackerel · Marine resources · Short tandem repeat · Population genetics · Conservation
Introduction The narrow barred Spanish mackerel S. commerson (Lacepede, 1800) is an important high valued epipelagic species, belonging to family Scombridae. They form a major fishery in coastal tropical waters of the Indo-Pacific region [1]. The
fish is mainly exploited by gill nets, trawls, hook and line, boat seines, shore seines and purse seines [2]. S. commerson is categorized as ‘Near Threatened’ as per IUCN conservation categorization. The capture production of this species in Indian waters is 30170 tonnes [3]. The peculiarity of S. commerson fishery is that quite large proportion of the catch
* PR Divya [email protected]
Rajeev Kumar Singh [email protected]
Linu Joy [email protected]
Vindhya Mohindra [email protected]
Sunitha Paulose [email protected]
Kuldeep Kumar Lal [email protected]
Charan Ravi [email protected]
1
PMFGR Centre, ICAR NBFGR, Kochi, India
2
ICAR National Bureau of Fish Genetic Resources, Lucknow,
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