title: De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, Silonia silondia (Hamilton, 1822) and their validation for population genetic studies.
abstract: The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity-capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6-24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall FST = 0.075; P < 0.0001) with maximum variation (92.5%) within populations. Cross-priming assessment revealed successful amplification (35-38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.
authors.affiliation: National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, Uttar Pradesh, 226002, India.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Mandal
authors.affiliation: National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, Uttar Pradesh, 226002, India.
authors.forename: J K
authors.initials: JK
authors.lastname: Jena
authors.affiliation: National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, Uttar Pradesh, 226002, India. rajeevsingh1@yahoo.com.
authors.forename: Rajeev K
authors.identifier: http://orcid.org/0000-0002-7355-0412
authors.initials: RK
authors.lastname: Singh
authors.affiliation: National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, Uttar Pradesh, 226002, India.
authors.forename: Vindhya
authors.initials: V
authors.lastname: Mohindra
authors.affiliation: Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra, 40006, India.
authors.forename: W S
authors.initials: WS
authors.lastname: Lakra
authors.affiliation: Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra, 40006, India.
authors.forename: Geetanjali
authors.initials: G
authors.lastname: Deshmukhe
authors.affiliation: National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, Uttar Pradesh, 226002, India.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Pathak
authors.affiliation: Network of Aquaculture Centres in Asia-Pacific, Bangkok, 10900, Thailand.
authors.forename: Kuldeep K
authors.initials: KK
authors.lastname: Lal
mesh_terms: D000483:Alleles; D000818:Animals; D002397:Catfishes / Q000235:genetics*; D029941:Fish Proteins / Q000235:genetics*; D056426:Genetic Loci; D005828:Genetics, Population; D016678:Genome; D015698:Genomic Library; D005838:Genotype; D006579:Heterozygote; D007194:India; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D045483:Rivers; D013045:Species Specificity; D013785:Thailand
chemical_list: D029941:Fish Proteins
keywords: Cross-species amplification; Microsatellite loci; Polymorphic; Population genetics; Silonia silondia