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

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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.

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Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (no. 2011AA100402), the Ministry of Agriculture introduced project (2011-G12), and the National Infrastructure of Fishery Germplasm Resources.

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Authors and Affiliations

  1. National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.43, Songfa Street, Daoli District, Harbin, 150070, Heilongjiang, China

    Xianhu Zheng, Youyi Kuang, Weihua Lü, Dingchen Cao & Xiaowen Sun

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  1. Xianhu Zheng
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  2. Youyi Kuang
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  3. Weihua Lü
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  4. Dingchen Cao
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  5. Xiaowen Sun
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Corresponding author

Correspondence to Xiaowen Sun.

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Appendix

Appendix

A list of the 151 EST–SSRs is presented in Table S1, including the primer sequences, repeat motif structure, expected size of amplification product, annealing temperature, and GenBank accession numbers. Segregation analysis of the 151 EST–SSRs in a full-sib family is presented in Table S2.

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Zheng, X., Kuang, Y., Lü, W. et al. Transcriptome-derived EST–SSR markers and their correlations with growth traits in crucian carp Carassius auratus . Fish Sci 80, 977–984 (2014). https://doi.org/10.1007/s12562-014-0782-2

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  • DOI: https://doi.org/10.1007/s12562-014-0782-2

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