Microsatellite maker analysis reveals the low genetic diversity in an endangered fish, Osteobrama belangeri in the Indo-Myanmar region

Abstract

Abstract Background Pengba (Osteobrama belangeri) is a medium carp endemic to Manipur with favorable characteristics for poly-culture and a great demand for its texture. Moreover, pengba is listed as a Near-threatened species according to the IUCN and the study on genetic characterization of this species is scanty. The lack of studies on the population structure of this species is significant from the conservation point of view, thus the present study aimed to validate selected anonymous and gene-associated (growth and sex-traits related) microsatellites obtained by whole genome sequencing using Illumina next-generation sequencing. Results In general, the evaluation of 106 markers resulted in 13 polymorphic loci, of which 7 were gene-associated and 6 were anonymous using Whole Genome Sequenced data of O. belangeri. The mean observed heterozygosity of culture and wild populations ranged from 0.050 to 0.850 and expected heterozygosity ranged from 0.095 to 0.728, respectively. The grand average of the number of alleles (Na) and the number of effective alleles (Ne) are 2.192 and 1.602. Conclusion This study infers a significant lack of genetic diversity due to low heterozygosity in the culture and wild populations of Osteobrama belangeriwhere irresponsible ranching could be a reason. Additionally, the developed polymorphic microsatellites in the current study are the first molecular markers available for genetic studies in O. belangeri, which could be used for the construction of a genetic map and search for Quantitative Trait Loci (QTL) which ultimately helps in Molecular Assisted Selection (MAS) in the future studies.