Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusc important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing OA, whereas a captive-raised population sourced from a region of weaker upwelling exhibited significant mortality and vulnerability to OA. This difference was linked to population-specific variation in the maternal provisioning of lipids to offspring, with a positive correlation between lipid concentrations and survival under OA. This relationship also persisted in experiments on second-generation animals, and larval lipid consumption rates varied among paternal crosses, which is consistent with the presence of genetic variation for physiological traits relevant for OA survival. Across experimental trials, growth rates differed among family lineages, and the highest mortality under OA occurred in the fastest growing crosses. Identifying traits that convey resilience to OA is critical to the continued success of abalone and other shellfish production, and these mitigation efforts should be incorporated into breeding programs for commercial and restoration aquaculture.

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.

The reproductive status in abalone (Haliotis spp.) can be difficult to discern using traditional visual inspection methods and may therefore rely on lethal histological analyses for a definitive determination. With endangered species of abalone, lethal histological examinations are strictly prohibited due to their imperiled status. This research investigated the effectiveness of using non-invasive ultrasound technology as an alternate means of identifying the reproductive status of abalone rather than through invasive biopsies or lethal histological methods. Twelve abalone were randomly selected from cultured red abalone broodstock cohort (n = 200) produced at The Cultured Abalone Farm (Goleta, CA) to initially test these methods. Following initial gonad ultrasound determination, a subset of another cohort of 5 year-old (n = 62) red abalone produced at the UC Davis Bodega Marine Laboratory were monitored using ultrasonography to detect seasonal changes in gonad size for 7 weeks. Following the 7-week assessment period, the full cohort of 5-year old abalone (n = 122) were then spawned and gonads were also evaluated using ultrasound technology before and immediately after spawning. Ultrasound imaging technology accurately differentiated between digestive and reproductive tissues, allowing for the characterization of an ultrasound gonad index score for rapid assessment. Mean gonad thickness determined via ultrasound imaging was categorized on a scale of 1–5, with an index of 1 being the lowest (gonad tissue thin or absent) and an index of 5 being the highest (gonad margin has increased and is compressing the digestive gland) for red abalone. Ultrasound imaging technology was successful in rendering a gonad index score that can be used to track gonad maturation over time in cultured or captive species. Tracking ultrasound gonad scores over time is a useful tool for improving abalone culture production, and increasing animal welfare by reducing handling stress associated with gonad assessments. Individual abalone that are empirically determined ready to be spawned can then be selected for broodstock. Non-invasive ultrasound technology has the potential for broad applications within abalone aquaculture to enhance both food and conservation aquaculture breeding programs.

IntroductionBlack (H. cracherodii) and white abalone (H. sorenseni) are federally listed as endangered species in the United States. Conservation efforts include captive breeding programs; however, determination of the reproductive state of individual abalone is notoriously difficult using traditional visual assessments. Ultrasonography is a well-recognized technology used to assess gonad reproductive condition accurately and nonlethally in cultured and wild fish, and more recently cultured red abalone (H. rufescens). Here, we implemented the use of ultrasound imaging technology to monitor the gonad condition of endangered black and white abalone.MethodsRepeated ultrasound assessments of the gonad were used to assess seasonal changes in reproductive development in wild black (n=20), and captive white abalone (n=25).ResultsA modified ultrasound gonad index score was developed to incorporate multiple species of abalone. The ultrasound index scores ranged from one to five, with an index score of one being the lowest (gonad margin is thinly wrapped around the digestive gland or not present) and an index score of five being the highest (gonad margin is thick and significantly compressing the digestive gland).ConclusionWe show that non-lethal ultrasound imaging technology is useful for tracking cyclical changes in the gonad reproductive condition as well as a more precise selection of individuals that are in peak reproductive condition for captive breeding programs.