Analysis of genetic diversity of Leuciscus leuciscus baicalensis using novel microsatellite markers with cross-species transferability

Abstract

ABSTRACT. We used next-generation sequencing technology to characterize 19 genomic simple sequence repeat (SSR) markers and 11 expressed sequence tag (EST) SSR markers from Leuciscus leuciscus baicalensis, a small freshwater fish that is widely distributed in Xinjiang, China. Primers were used to test for polymorphisms in three L. leuciscus baicalensis populations in Xinjiang. There were 4-27 (average 11.3) alleles (N A ), the expected heterozygosity (H E ) was 0.36-0.94 (average 0.75 ± 0.14), the observed heterozygosity (H O ) was 0.37-1.00 (average 0.68 ± 0.18), and the polymorphism information content (PIC) was 0.31-0.93 (average 0.71). The averages of H E and PIC for the EST-SSR markers were slightly lower than for the genomic SSR markers. Genetic analysis of the three populations showed similar results for PIC, H E , and N A . Amplifications were performed in nine other species; the top three transferability values were for Rutilus lacustris baicalensis is one of the most important commercial fish in Xinjiang, but in recent years, fishery resources have decreased sharply owing to water conservation projects, unreasonable utilization, and invasion by alien species. These novel SSR markers are appropriate for studies involving fingerprinting, gene flow, genetic diversity, population structure, and molecular-assisted breeding, and could contribute to the conservation of L. leuciscus baicalensis.

Development of an effective microsatellite marker system to determine the genetic structure of <i>Meriones meridianus</i> populations

“…Because the whole genome of Meriones meridianus has not been sequenced completely, it is difficult to obtain suitable microsatellite markers by genome sequencing. It has been reported that cross-species amplification of species microsatellite loci in related species is an effective way to isolate microsatellite markers [14,15,22,24]. Since the midday gerbils and Mongolian gerbils are the closely related species, the present study aimed to identify microsatellite loci for Meriones meridianus on the basis of a significant microsatellite marker system (28 loci markers) using the method of cross-amplification of species, which has already been established for the Mongolian gerbil [8].…”