Development and Utilization of Transcriptome SSR Markers in <em>Procambarus clarkii</em>

Abstract

To accelerate the research process of molecular marker-assisted breeding in <em>Procambarus clarkii</em>, this study conducted transcriptome sequencing of <em>P. clarkii</em> muscle tissue using the Illumina NovaSeq platform. Microsatellites (SSRs) were analyzed for distribution and sequence characteristics using MIcroSAtellite (MISA), and genetic diversity was studied in seven cultured populations. The results showed that the sequencing yielded between 9.9 to 12.7 Gb of clean data, and after assembly, produced between 52,244 to 83,367 contigs, identifying a total of 11,304 SSR loci. The SSRs were predominantly dinucleotide and trinucleotide repeats, accounting for 33% and 27% of the total loci, respectively. The average observed heterozygosity (Ho) across the seven different regional aquaculture populations ranged from 0.374 to 0.502, while the average expected heterozygosity (He) ranged from 0.502 to 0.604. The average polymorphic information content (PIC) for the populations was greater than 0.450, indicating substantial genetic variability. According to Nei's genetic distance, an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster tree divided the seven different regional aquaculture populations into two major clades: one comprising Yunnan (YN) and Qianjiang (QJ) and the other comprising the remaining five populations. The study found that 93.52% of the variation originated within populations, with only 6.48% of genetic variation attributable to differences between populations. These results lay a foundation for further assessment of the genetic diversity of <em>P. clarkii</em>, innovative utilization of germplasm resources, and in-depth studies into its molecular genetics and evolutionary mechanisms.