Development of genetic markers in abalone through construction of a SNP database

Seasonal changes in gene expression and polymorphism of hsp70 in cultivated oysters (Crassostrea gigas) at extreme temperatures

The HSP70 proteins are an important element of the response against thermal stress and infectious diseases, and they are highly conserved and ubiquitous. In some species, variations on the hsp70 encoding sequence resulted in intraspecific differential expression, which leads to variations on thermo-tolerance among individuals. This phenomenon has not been described in the Pacific oyster Crassostrea gigas, which is cultivated in Mexico under temperature conditions highly above the optimal for this species. The present study was aimed to identify associations between hsp70 genotypes and their expression levels in C. gigas. By analyzing a 603 bp fragment from the 3' end of the hsp70 gene, 21 different genotypes with 60 nucleotide polymorphic sites were detected, of which 34 sites were found in heterozygous condition. Although no correlation was found between genotype-expression-season, a minimum expression threshold that should be taken into account as an important feature for a future breeding program is proposed.

Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays

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.

SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens

The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects.

Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants sea cucumber (Apostichopus japonicus)

Color variation is a well-known feature of sea cucumbers (Apostichopus japonicus), which are classified into three groups based on their colors of red, green and black. It is also one of the most important traits related to how they taste, and it thereby affects their market price. Attempts were made to identify single-nucleotide polymorphisms (SNPs) and to analyze differences associated with SNP genotypes between green and red color variants using HSP70 as the target gene. The HSP70 gene, which is found universally in organisms from bacteria to humans, is one of the most evolutionarily conserved genes and the most widely studied biomarker of stress response. DNA fragments of 1074 bp covering a partial sequence of the sea cucumber HSP70 gene, were amplified from both red and green variants, and subsequently analyzed for the presence of SNPs. Twenty-seven polymorphic sites in total, including heterozygous sites, were observed. Of these, six sites were found to be significantly different SNP genotypes between green and red variants. Furthermore, PCR with an internal primer designed to include an allele-specific SNP at the 3' end (site 443) showed differentiation between the two variants, 100% and 4.2% amplification in green and red variants, respectively. The validated SNPs may serve as informative genetic markers that can be used to distinguish variants at the early developmental stage, prior to color differentiation.