Microsatellite Markers to Determine Population Genetic Structure in the Golden Anchovy, Coilia dussumieri

Abstract

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

Identification and characterisation of microsatellite markers in narrow barred Spanish mackerel Scomberomorous commerson (Lacepede, 1800)

“…High microsatellite allele variation observed in the study was comparable with previous findings in marine fishes including Atlantic cod (8-46 alleles per locus) (Bentzen et al, 1996), silver pomfret (13-17 alleles per locus) (Archangi et al, 2013) and Atlantic salmon (5-41 alleles per locus; Nikolic et al, 2009) (Table 4). The observed allele frequencies in most of the loci did not show significant deviation (p>0.05) from Hardy-Weinberg equilibrium after sequential Bonferroni correction, which was similar to results in earlier studies (Kathirvelpandian et al, 2014;Mohitha et al, 2014). Wright's (1978) fixation index (F IS ) is a measure of heterozygote deficiency or excess (inbreeding co-efficient) and the values of F IS for all populations ranged from -0.150 for the locus Sa 2657 to + 0.694 for locus Sa 2873.…”

“…Flanking region similarities or conserved regions between closely related species helps to reduce the effort required for designing primers in other marine fish species (Kathirvelpandian et al, 2014;Mohitha et al, 2014). The success of cross-species amplification is higher for species with long generation time, mixed or out crossing breeding system and smaller genome size compared to the resource species (Barbara et al, 2007).…”

“…Fortunately, flanking region similarities between closely related species reduces considerable effort for developing polymorphic microsatellite markers for population genetic analysis (cross-species amplification). This cost-effective alternative for developing polymorphic microsatellite markers is comparatively easier and has been successfully carried out in many fish species for population studies (Lal et al, 2004;Mohitha et al, 2014;Kathirvelpandian et al, 2014). In the present study, development of 11 microsatellite markers in S. commerson through cross-species amplification was carried out from closely related species such as Scomber australasicus, Scomber japonicus, Scomberomorus cavalla and Rastrelliger kanagurta.…”

Stock discrimination ofSperata aorfrom river Ganga using microsatellite markers: implications for conservation and management

“…Genetic variation analysis using microsatellite markers demands species-specific primers but cross-species amplification of existing primers of closely related species can also be employed successfully. Cross-species amplification is utilized due to the fact that many microsatellite loci surrounded by flanking regions are conserved among closely related species despite high mutation rate (Kathirvelpandian et al, 2014). The low rate of evolutionary divergence among the closely related species justifies the success of cross-species amplification (Gupta et al, 2013).…”