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Development of gene-targeted SNP markers for genomic mapping in Pacific abalone Haliotis discus hannai Ino

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Abstract

Useful and novel DNA markers are needed for aquaculture genetics and breeding. In this study, we report the discovery and development of gene-targeted single nucleotide polymorphisms (SNPs) for genomic mapping in the Pacific abalone Haliotis discus hannai Ino. Single EST or EST-contigs from 66 genes that had positive BLASTx matches (E-value ≤ 1e-8) were used for polymerase chain reaction (PCR) amplification. PCR products from the two parents of one mapping family were directly sequenced, and 83 SNP loci were found from 17 genes. Allele-specific PCR (AS-PCR) was developed and optimized for genotyping of 11 SNP loci in 120 progeny of the mapping family. Nine of the loci conformed to the expected Mendelian ratio of 1:1 based on the χ2 test (P > 0.05) and could potentially be used for linkage map construction. Our data also indicate that the sequencing of two parents may be a practical strategy for the discovery of informative SNPs for linkage mapping in a particular mapping population.

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Acknowledgments

This research was funded by grants from National High Technology Research and Development Program of China (863 Program) (No. 2006AA10A407) and National Basic Research Program of China (973 Program) (No. 2010CB126402).

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Authors and Affiliations

  1. Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China

    Haigang Qi, Xiao Liu, Fucun Wu & Guofan Zhang

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  1. Haigang Qi
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  2. Xiao Liu
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  4. Guofan Zhang
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Correspondence to Guofan Zhang.

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Qi, H., Liu, X., Wu, F. et al. Development of gene-targeted SNP markers for genomic mapping in Pacific abalone Haliotis discus hannai Ino. Mol Biol Rep 37, 3779–3784 (2010). https://doi.org/10.1007/s11033-010-0032-3

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