Evaluation of six sugar kelp crosses selected for high yield at three Northeastern US farms
Not Available
Gonzalez, Sara T.↗
Engineering topics
Yarish, Charles
Publications and source records attributed to Yarish, Charles.
Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima
Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.
DeWeese, Kelly↗
Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study
Introduction Sugar kelp ( Saccharina latissima ) has a biphasic life cycle, allowing selection on both thediploid sporophytes (SPs) and haploid gametophytes (GPs). Methods We trained a genomic selection (GS) model from farm-tested SP phenotypic data and used a mixed-ploidy additive relationship matrix to predict GP breeding values. Topranked GPs were used to make crosses for further farm evaluation. The relationship matrix included 866 individuals: a) founder SPs sampled from the wild; b) progeny GPs from founders; c) Farm-tested SPs crossed from b); and d) progeny GPs from farm-tested SPs. The complete pedigree-based relationship matrix was estimated for all individuals. A subset of founder SPs ( n = 58) and GPs ( n = 276) were genotyped with Diversity Array Technology and whole genome sequencing, respectively. We evaluated GS prediction accuracy via cross validation for SPs tested on farm in 2019 and 2020 using a basic GBLUP model. We also estimated the general combining ability (GCA) and specific combining ability (SCA) variances of parental GPs. A total of 11 yield-related and morphology traits were evaluated. Results The cross validation accuracies for dry weight per meter ( r ranged from 0.16 to 0.35) and wet weight per meter ( r ranged 0.19 to 0.35) were comparable to GS accuracy for yield traits in terrestrial crops. For morphology traits, cross validation accuracy exceeded 0.18 in all scenarios except for blade thickness in the second year. Accuracy in a third validation year (2021) was 0.31 for dry weight per meter over a confirmation set of 87 individuals. Discussion Our findings indicate that progress can be made in sugar kelp breeding by using genomic selection.
59 BASIC BIOLOGICAL SCIENCES↗
Estimating production cost for large-scale seaweed farms
Seaweed farming has the potential to produce feedstocks for many applications, including food, feeds, fertilizers, biostimulants, and biofuels. Seaweeds have advantages over land-based biomass in that they require no freshwater inputs and no allocation of arable land. To date, seaweed farming has not been practiced at scales relevant to meaningful biofuel production. Here we describe a techno-economic model of large-scale seaweed farms and its application to the cultivation of the cool temperate species Saccharina latissima (sugar kelp) and the tropical seaweed Eucheumatopsis isiformis. At farm scales of 1000 ha or more, our model suggests that farm gate production costs in waters up to 200 km from the onshore support base are likely to range between $\$$200 and $\$$300 per dry tonne. The model also suggests that production costs below $\$$100 per dry tonne may be achievable in some settings, which would make these seaweeds economically competitive with land-based biofuel feedstocks. While encouraging, these model results and some assumptions on which they are based require further field validation.
09 BIOMASS FUELS↗
Skinny kelp (Saccharina angustissima) provides valuable genetics for the biomass improvement of farmed sugar kelp (Saccharina latissima)
Abstract Saccharina latissima (sugar kelp) is one of the most widely cultivated brown marine macroalgae species in the North Atlantic and the eastern North Pacific Oceans. To meet the expanding demands of the sugar kelp mariculture industry, selecting and breeding sugar kelp that is best suited to offshore farm environments is becoming necessary. To that end, a multi-year, multi-institutional breeding program was established by the U.S. Department of Energy's (DOE) Advanced Research Projects Agency-Energy (ARPA-E) Macroalgae Research Inspiring Novel Energy Resources (MARINER) program. Hybrid sporophytes were generated using 203 unique gametophyte cultures derived from wild-collected Saccharina spp . for two seasons of farm trials (2019–2020 and 2020–2021). The wild sporophytes were collected from 10 different locations within the Gulf of Maine (USA) region, including both sugar kelp ( Saccharina latissima ) and the skinny kelp species ( Saccharina angustissima ). We harvested 232 common farm plots during these two seasons with available data. We found that farmed kelp plots with skinny kelp as parents had an average increased yield over the mean (wet weight 2.48 ± 0.90 kg m −1 and dry weight 0.32 ± 0.10 kg m −1 ) in both growing seasons. We also found that blade length positively correlated with biomass in skinny kelp x sugar kelp crosses or pure sugar kelp crosses. The skinny x sugar progenies had significantly longer and narrower blades than the pure sugar kelp progenies in both seasons. Overall, these findings suggest that sugar x skinny kelp crosses provide improved yield compared to pure sugar kelp crosses.
59 BASIC BIOLOGICAL SCIENCES↗
Evaluation of nutrient bioextraction by seaweed and shellfish aquaculture in Korea
Abstract Although Korea is third in seaweed production and second in shellfish production globally, this is the first study evaluating ecosystem services of seaweed and shellfish aquaculture in Korea. The objective of this study is to evaluate nutrient bioextraction capacities of major seaweed and shellfish species aquacultured in Korea. C (C) removal of three major aquacultured seaweed species, Neopyropia yezoensis , Saccharina japonica , and Undaria pinnatifida were 24,247, 8,423, and 12,758 tons, respectively, in 2016. N (N) removal of these species was 4,088, 732, and 1,244 tons, respectively. The C and N removal of the Pacific oysters ( Crassostrea gigas ) were 14,693 and 1,050 tons, respectively. Manila clams ( Venerupis philippinarum ) removed 2,120 tons of C and 136.5 tons of N. Together, 161,846 tons of CO 2 and 7,251 tons of N were removed by three major seaweed species and two shellfish species. These values are significant amounts, equivalent to 5.7% of CO 2 and 8.6% of N discharged from all wastewater treatment plants in Korea. These results suggest that nutrient bioextraction by aquacultured seaweed and shellfish can be a cost efficient, affordable, and equitable solution for coastal nutrient management programs in Korea and elsewhere.
Park, Ji‐Sook↗
Germplasm cryopreservation of macroalgae for aquaculture breeding and natural resource conservation: A review
The expansion of the global macroalgal aquaculture and climate change creates the need for germplasm preservation of valuable aquaculture strains and maintenance of natural biodiversity. Compared to the large number of studies in fish and shellfish species, relative few studies have been conducted on the macroalgal germplasm cryopreservation. The first cryopreservation of macroalgae to –75 °C was reported on Neopyropia tenera (formerly called Porphyra tenera) in 1964. To date, a total of 34 studies reported germplasm cryopreservation in 33 species, including Chlorophyta (7 species), Ochrophyta (14 species), and Rhodophyta (12 species). Here, the goal of this review was to summarize the published studies on macroalgal germplasm cryopreservation, compare the reported protocols for the cryopreservation process, and identify the factors affecting post-thaw viability. Overall, macroalgal germplasm cryopreservation included haploid or diploid thalli, spores, and gametes. Cryotubes (1.5-ml or 2-ml) have been widely used to package germplasm samples for cooling and storage in most studies, and the 0.5-ml straws and 5-ml cryotubes have been used in several studies. Two approaches (programmable controlled cooling and vitrification) were employed for macroalgal germplasm cryopreservation. A two-step programmable controlled cooling (e.g., from initial culture temperature to a frozen temperature, such as –40 °C, and then directly plunging into liquid nitrogen at –196 °C) was determined to be an effective cooling strategy. Vitrification, a super rapid cooling for a sample to form non-crystalline amorphous solid, was applied on macroalgal germplasm cryopreservation with sample encapsulation and dehydration. Survival of post-thaw samples varied significantly in different studies. Based on research updates, recommendations are made for future research. It is expected that this review can serve as a foundation for future germplasm banking of macroalgae for aquaculture and biodiversity preservation.
59 BASIC BIOLOGICAL SCIENCES↗
Restoring Pre-Industrial CO2 Levels While Achieving Sustainable Development Goals
Unless humanity achieves United Nations Sustainable Development Goals (SDGs) by 2030 and restores the relatively stable climate of pre-industrial CO2 levels (as early as 2140), species extinctions, starvation, drought/floods, and violence will exacerbate mass migrations. This paper presents conceptual designs and techno-economic analyses to calculate sustainable limits for growing high-protein seafood and macroalgae-for-biofuel. We review the availability of wet solid waste and outline the mass balance of carbon and plant nutrients passing through a hydrothermal liquefaction process. The paper reviews the availability of dry solid waste and dry biomass for bioenergy with CO2 capture and storage (BECCS) while generating Allam Cycle electricity. Sufficient wet-waste biomass supports quickly building hydrothermal liquefaction facilities. Macroalgae-for-biofuel technology can be developed and straightforwardly implemented on SDG-achieving high protein seafood infrastructure. The analyses indicate a potential for (1) 0.5 billion tonnes/yr of seafood; (2) 20 million barrels/day of biofuel from solid waste; (3) more biocrude oil from macroalgae than current fossil oil; and (4) sequestration of 28 to 38 billion tonnes/yr of bio-CO2. Carbon dioxide removal (CDR) costs are between 25–33% of those for BECCS with pre-2019 technology or the projected cost of air-capture CDR.
54 ENVIRONMENTAL SCIENCES↗
Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers
An assessment of genetic diversity of marine populations is critical not only for the understanding and preserving natural biodiversity but also for its commercial potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, FST, admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is more heterogeneous than SNE. These two regions have large genetic difference (between-location FST ranged from 0.21 to 0.32) and were separated by Cape Cod, which is known to be the biogeographic barrier for other taxa. We detected one significant SNP (P = 2.03 × 10 -7 ) associated with stipe length, and 248 SNPs with higher-than-neutral differentiation. The findings of this study provide baseline knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for future commercialization opportunities.
54 ENVIRONMENTAL SCIENCES↗
Macroalgal germplasm banking for conservation, food security, and industry
Ex situ seed banking was first conceptualized and implemented in the early 20th century to maintain and protect crop lines. Today, ex situ seed banking is important for the preservation of heirloom strains, biodiversity conservation and ecosystem restoration, and diverse research applications. However, these efforts primarily target microalgae and terrestrial plants. Although some collections include macroalgae (i.e., seaweeds), they are relatively few and have yet to be connected via any international, coordinated initiative. In this piece, we provide a brief introduction to macroalgal germplasm banking and its application to conservation, industry, and mariculture. We argue that concerted effort should be made globally in germline preservation of marine algal species via germplasm banking with an overview of the technical advances for feasibility and ensured success.
59 BASIC BIOLOGICAL SCIENCES↗
The application of flow cytometry for kelp meiospore isolation
The goal of this study was to evaluate flow-cytometric techniques for isolating individual kelp meiospores into 96-welled plates. Previously reported low success rates for sorting tens of thousands of meiospores at a time have been improved by technological developments, specifically, the low nozzle pressure of the commercially available, JSAN (Bay Bioscience Co. Ltd) instrument. We monitored growth and gametophyte development post-sorting for 10 months. Our data demonstrate that successful kelp meiospore isolations of up to 76% viability can be achieved with flow-cytometry. This method can save time as compared to traditional, manual isolations using pipettes and improves confidence that self-fertilized individuals will not contaminate specific crosses of resulting gametophytes. Our results highlight a new application for the flow cytometer to produce clonal kelp gametophytes with direct applications for germplasm and culture collection development.
59 BASIC BIOLOGICAL SCIENCES↗