Development and Characterization of RAPD and Microsatellite Markers for Genetic Variation Analysis in the Critically Endangered Yellow Catfish Horabagrus nigricollaris (Teleostei: Horabagridae)

Abstract

Random-amplified polymorphic DNA (RAPD) and microsatellite markers were developed and used for the analysis of genetic variability in the critically endangered yellow catfish Horabagrus nigricollaris, sampled from the Chalakkudy River, Kerala, India. Eight RAPD and five microsatellite markers were detected to genotype the species. In RAPD, the 73 fragments were 20.55% polymorphic, whereas 4 polymorphic loci (80%) were obtained in microsatellites. In microsatellites, the number of alleles across the 5 loci was 1-5, and the range of heterozygosity was 0.25-0.5. The mean observed number of alleles was 2.4, and the effective number was 1.775 per locus. The average heterozygosity across all investigated samples was 0.29, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods report a low degree of gene diversity and lack of genetic heterogeneity in the population of H. nigricollaris, emphasizing the need for fishery management, conservation, and rehabilitation of this species.

Genetic characterization of native and invasive Plagioscion squamosissimus (Perciformes, Sciaenidae) populations in Brazilian hydrographic basins

“…The level of genetic differentiation between the population native to the Parnaíba River basin and the population native to the Araguaia-Tocantins River basin is consistent with level of intraspecies genetic differentiation estimated for other fish species, including neotropical species (Silvia et al, 2008;Muneer et al, 2011). For instance, genetic differentiation as inferred from RAPD markers was relatively low between two Pseudoplatystoma corruscans populations isolated by the former Guaíra Falls in the Paraná River basin (Sekine et al, 2002).…”

“…Since these primers do not discriminate between coding and noncoding DNA sequences, the RAPD technique samples the genome in a highly randomized manner, and innumerable anonymous loci may be amplified (Williams et al, 1990). RAPD has been successfully used in fishes to establish phylogenetic relationships (Roy et al, 2014), to study interspecific hybridization (Oliveira et al, 2002;Sovic et al, 2012), and to study the genetics of populations and sub-populations (Muneer et al, 2011;Sivaraman et al, 2014).…”

Genetic characteristics of Tambaqui broodstocks in the state of Rondônia, Brazil: implications on production and conservation

“…Low genetic diversity is negatively correlated with adaptation potential to changes in environmental conditions (RASHID et al, 2012;LYNCH et al, 1995;LOEW, 2000). Management and conservation strategies may be successfully planned when correct information exists on the genetic composition of the species (MUNEER et al, 2011).…”

PICcalc: An Online Program to Calculate Polymorphic Information Content for Molecular Genetic Studies

“…Marker systems differ in their information content, which depends on polymorphism. The concept of polymorphism is used to define genetic variation in a population, which has been extensively studied in recent years by several established scientific disciplines, for example, genetics, ecology, zoology, and microbiology (Mukherjee et al 2010;Muneer et al 2011;Rajkumar et al 2011). Examples are numerous and obvious.…”