GENETIC STRUCTURE OF CHINESE CARPS IN PUNJAB AS REVEALED BY DNA MARKERS

Abstract

Genetic integrity of commercially important fishes is integral to sustainable fisheries. The conventional propagation practices and human interventions in the natural aquatic resources are leading to genetic degradation of fish stocks at various scales. The Chinese carps like other related species are prone to genetic deterioration that may result in perspective local extinctions. The present study evaluated the extent of genetic variability and assessed the population structure of Chinese carps viz. Silver Carp (Hypophthalmichthys molitrix) and Grass Carp (Ctenopharyngodon idella) in hatchery and wild stocks in response to conventional breeding and practices human perturbations. For this, the sample of the appraisal species were collected from selected sites in different districts of Punjab. At least, thirty specimens of each species were collected from each hatchery and natural stock. The genomic DNA of good quality was isolated from the dorsal muscles of the fish. Sixteen species-specific polymorphic microsatellite markers for each species were employed to genotype the individual fish at the target loci by using PCR. For genotyping the PCR amplicons were resolved on polyacrylamide gel electrophoresis followed by gel imaging and the allelic scoring was done on manual basis. The genotypic data was subjected to rigorous analyses in different programs i.e. Popgen, FStat, TFPGA, STRUCTURE and ARLEQUIN to infer various indices of genetic variability and structuring in populations of Chinese carps. The results revealed low-to-moderate scale genetic variability in the hatchery stocks while the same was moderate-to-high in riverine stocks for both the species. In the hatchery populations of Silver Carp, a total of 77 different alleles varied from 2 to 12 across all the loci. The level of average observed heterozygosity was low-to-moderate and varied from 0.3771 to a maximum of 0.5874 in the hatchery stocks while the same ranged between 0.50 and 0.6354 for wild populations. Most of the hatcheries showed heterozygote deficit. The average values of inbreeding coefficient varied from 0.174 to 0.441 with negative values for some hatcheries indicating possible outbreeding. The corresponding values of observed heterozygosity were higher for the riverine stocks. The AMOVA reveled significant genetic structuring both in hatchery and riverine populations of Silver Carp. The UPGMA dendrogram showed the populations clustering irrespective of their geographical proximities. In the populations of Grass Carp, the allelic number ranged from 4 to 15 across all the loci. In the hatcheries, the values of average observed heterozygosity varied between 0.4583 to a maximum of 0.6104. The corresponding values for riverine stocks were found to vary from 0.4791 to 0.6354. The inbreeding coefficient varied between 0.2632 - 0.4651 for hatcheries and 0.2909 - 0.3438 for the riverine populations of Grass Carp. Like Silver Carp, the negative values in several populations of Grass Carp revealed possible outbreeding/crossbreeding. Out of 128 tests, 88 deviated from HWE significantly in all the hatchery populations and the same was 58 for riverine stocks of Grass Carp. The results of AMOVA indicated that most of the variation existed at the intra-population level, pointing out significant genetic structuring in the hatchery as well riverine populations. The UPGMA dendrograms did not follow the geographical patterns of the Grass Carp populations showing human mediated/restricted gene flow. Overall, both the Chinese carps underwent loss of alleles as compared to the native populations. The population structure of the species has been shaped by the hydrographic and anthropogenic factors. Incorporating the current information on genetic structure of the species could be helpful for effective management and conservation of Chinese carps in Pakistan