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

• Published in: Molecular biology reports Vol. 47; no. 12; pp. 10005 - 10014
• Main Authors: Joy, Linu, Paulose, Sunitha, Divya, PR, Ravi, Charan, Basheer, VS, Kumar, Rajesh, Singh, Rajeev Kumar, Mohindra, Vindhya, Lal, Kuldeep Kumar
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-12-2020; Springer Nature B.V
• Subjects: Animal Anatomy; Animal Biochemistry; Biomedical and Life Sciences; Fish; Fisheries; Fishing; Genetic analysis; Genetic diversity; Genetic markers; Genotyping; Geographical distribution; Histology; Life Sciences; Microsatellites; Molecular biology; Morphology; Population; Population genetics; Population studies; Scomberomorus commerson; Scomberomorus guttatus; Short Communication; Software; Species; Thermal cycling; Spanish mackerel; Marine resources; Population genetics; Short tandem repeat; Conservation
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-020-05975-6

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
.