Transcriptome-derived EST–SSR markers and their correlations with growth traits in crucian carp Carassius auratus

Abstract

In our previous study, transcriptomes of crucian carp were sequenced using 454 Sequencing, which generated many expressed sequence tag (EST) sequences that are useful to develop gene-based markers. In this study, from these ESTs, 5505 simple sequence repeats (SSRs) were identified, among which dinucleotide repeats (43.6 %) and AC/GT motifs (39.6 %) were the most frequent, followed by AAT/ATT (15.5 %). We designed 3932 primers with sufficient amplified flanking sequences. To verify the identified EST–SSRs, 500 primers were randomly selected for polymerase chain reaction (PCR), of which 408 (81.6 %) were successfully amplified, among which 151 (30.2 %) were polymorphic. These polymorphic markers were further surveyed among an F1 population. The results showed that 148 loci were informative in both parents, with segregation ratios of 1:1:1:1 (23, 15.5 %), 1:1 (59, 39.9 %), and 1:2:1 (66, 44.6 %). In addition, the general linear model (GLM) procedure in the SPSS software package was used to analyze the correlations between these 148 loci and two growth traits. Twelve loci were discovered to be significantly (P < 0.05 or P < 0.01) associated with body weight (BW), and 13 loci were significantly (P < 0.05 or P < 0.01) correlated with standard length (SL). Meanwhile, genotypes that favorably affect BW and SL traits were determined. Therefore, the EST–SSRs developed in this work may be useful in linkage map studies and for marker-assisted selection (MAS) in breeding programs of this species.