Genome-wide SSR marker development and application in genetic diversity analysis of the red swamp crayfish, Procambarus clarkii (Girard, 1852) in China

Abstract

Abstract The red swamp crayfish, Procambarus clarkii (Girard, 1852), is currently an economically important aquaculture animal. Its genetic basis has been scarcely reported, however, partly due to the absence of abundant molecular markers in the genome. In this study, Simple Sequence Repeat (SSR) loci were mined, based on genome survey sequencing via the next generation sequence of the red swamp crayfish. A total of 4897 SSR loci were identified, with the most abundant type being the di-nucleotide repeat motifs (75.2%), followed by tri- (20.4%), tetra- (3.8%), penta- (0.5%), and hexanucleotide (0.2%) repeats. In total, 1546 SSR markers were validated to be amplified, and 721 of these were identified as polymorphic SSR markers. Fifty polymorphic SSR markers were randomly selected for the identification of the genetic diversity of the 14 red swamp crayfish populations in China. The expected and observed heterozygosity and polymorphism information content were 0.39, 0.30, and 0.29, respectively, on average. The results indicated a medium genetic diversity among the 14 investigated populations. These probably cluster into three genetic populations. The current study provides abundant genetic markers and information on the 14 populations, which can be helpful for genetic diversity estimation and molecular breeding of the red swamp crayfish.