Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers

Jessica Vervalle, Juli Ann Hepple, Suzaan Jansen, Jana Du Plessis, Peizheng Wang, Clint Rhode, Rouvay Roodt-Wilding*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)


The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.

Original languageEnglish
Pages (from-to)89-103
JournalJournal of Shellfish Research
Issue number1
Publication statusPublished - Apr 2013
Externally publishedYes


  • abalone
  • Haliotis midae
  • linkage map
  • microsatellites
  • single nucleotide polymorphisms

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    Vervalle, J., Hepple, J. A., Jansen, S., Plessis, J. D., Wang, P., Rhode, C., & Roodt-Wilding, R. (2013). Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers. Journal of Shellfish Research, 32(1), 89-103.