Abstract
Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and single nucleotide (SNPs). Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%–69% conversion rate (percentage polymorphic markers) with a global genotyping success rate of 76%–85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174) were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50) located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.
Highlights
The South African abalone, Haliotis midae, is a highly valuable marine resource and one of almost30 commercially viable abalone species found worldwide [1]
We focused on the development of single nucleotide polymorphisms (SNPs) from transcriptome data previously described for H. midae following two bioinformatic pipelines
The total number of contigs that resulted from the CLC Genomics Workbench de novo assembly was 22,761, with an average length of 260 bp and an average contig coverage of 400 reads/contig
Summary
The South African abalone, Haliotis midae, is a highly valuable marine resource and one of almost30 commercially viable abalone species found worldwide [1]. The South African abalone, Haliotis midae, is a highly valuable marine resource and one of almost. The South African abalone industry, the largest outside Asia, currently has a total output of 1015.44 metric tons, valued at 355 million South. Mainly microsatellite markers (274) have been developed for H. midae using various enrichment and in silico techniques [4,5,6,7]. These markers have already proven to be very useful, they have limitations, including development time, size homoplasy and the presence of null alleles [4]. The focus has shifted towards the development of single nucleotide polymorphisms (SNPs) with 40 SNPs isolated far [8,9]
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