Identification and validation of simple sequence repeats (SSR) markers for yellowfin barbel (Luciobarbus xanthopterus) using RNA-Seq data

This research was conducted to identify and validate the simple sequence repeats (SSR) markers related to yellowfin barbel (Luciobarbus xanthopterus) using RNA-Seq data. After collecting the liver tissue, RNA was extracted from the samples. The samples were sequenced using the Illumina Novaseq 6000 platform. Trinity software (version 2.15.1) was used to reconstruct transcripts. Identification of SSR was done using the MISA web server. The primers needed in the polymerase chain reaction for 5 SSR markers were designed by PRIMER 3 software and validated using 45 yellowfin barbel. Transcript assembly by the Trinity program generated 941,894 unigenes and 1,768,662 transcripts. In this study, the examination of 1,276,825 sequences by MISA software led to the identification of 349,871 potential SSR markers. Among the SSRs, di- and trinucleotide repeats had the highest number of repetitions with 89.37% and 8.05%, respectively. From the 5 primers used, only two of them showed polymorphism. The expected and observed heterozygosity for the MN1359 locus were calculated as 0.785 and 0.147, and for the GM1371 locus given 0.770 and 0.093, respectively. Moreover, the chi-square test showed that population was not in Hardy-Weinberg equilibrium. The results of different genetic diversity criteria showed a decrease in diversity in yellowfin barbel. Generally, this research showed that the new SSRs can be helpful for molecular breeding, functional genomics studies, and the genetic diversity analysis of yellowfin barbel.