Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

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.

A novel transcriptome-derived SNPs array for tench (Tinca tinca L.)

“…In fact, as a transcriptome is directly associated with functional regions in a genome, transcriptome-derived SNPs can be informative for adaptive variation [ 24 – 26 ] and they can be used not only for assessing population genetic structure, but also for genomic selection for traits of interest to aquaculture such as growth, sex determination or disease resistance (e.g. [ 27 – 29 ]). Given these advantages, SNPs derived from transcriptomes have been widely discovered and studied in many fish species [ 29 – 42 ].…”

Genome Sequencing of Blacklip and Greenlip Abalone for Development and Validation of a SNP Based Genotyping Tool

“…This is changing with development of first draft reference genome assemblies for both pacific ( H. discuss hannai ; Nam et al, 2017) and greenlip abalone ( H. laevigata ; Botwright et al, unpublished). Further, generation of de novo transcriptomes ( H. tuberculate ; Harney et al, 2016, H. midae ; Bester-Van Der Merwe et al, 2013) and construction of large insert libraries ( H. diversicolor ; Jiang et al, 2016) is starting to provide the tools required for better management of breeding programs and the ability to investigate the biological basis of key traits.…”

Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata

“…Furthermore, SNPs can be derived from increasingly common expressed sequence data such as the short reads and transcriptomes generated during RNA-Seq experiments (De Wit et al, 2015), making the development of novel markers straightforward compared to microsatellites. Non-synonymous substitutions in SNPs from coding regions may help to identify candidate genes for marker assisted selection (Merwe et al, 2013), and more broadly can be used in genetic analyses to understand the structure of the population and manage the stock (Rhode et al, 2017).…”