Production of high-yielding Manila clam seed through family-based breeding and polyploidy selection

Aquaculture of marine bivalves is a sustainable food system that provides high-quality animal protein while supporting the coastal environment. The U.S. is a top producer of the Manila clam (Ruditapes philippinarum). The production of clams, however, has largely relied on seeds from wild broodstock and natural recruitment, leaving the industry vulnerable to ocean change. We propose to develop a breeding program for Manila clams taking advantage of superior performances of female, triploid clams. In Phase I, we tested the feasibility of producing pair-mated families and identifying sex-ratios in embryos. Twenty-six distinct families were produced and grown to the seed stage and are in on-farm trials to determine the relationship between yields and sex-ratios between families. In the Phase II effort, we propose to produce female-biased triploid clams by (1) screening 200 pair-crosses for female-biased families; (2) identifying sex-ratios in embryos as a biomarker for better yield potentials; (3) inducing triploidy in high-yielding families; (4) conducting on-farm trials to evaluate yield for different crosses. The research will engage shellfish growers through direct participation in on-farm trials, enable commercialization of high-yielding seed clams, and pave the way for a long-term breeding program for the species for the U.S. shellfish aquaculture industry. Breeding programs for Manila clams are urgently needed for the shellfish aquaculture industry on the U.S. West Coast where the Manila clam is the second largest crop by volume behind the Pacific oyster. In Phase II, we anticipate developing family lines of Manila clams that have improved farm yields compared with generic seed, resulting from combining increased growth rates in female clams with superior production characteristics of triploids. On-farm trials are expected to demonstrate the higher yield and further refine improvement by incorporation of farm conditions and desired traits. The experimental approach is based on systematic separation of phenotypic variation in growth, survival, and sex-ratio into different clam families. We will use a known biomarker feasible for identifying sex-ratios in embryos and a genomic DNA staining procedure for checking ploidy in larvae for early screening for families with higher growth potentials. Improved seed clams from this proposed research could increase the farm yield by 30% in a single generation and will directly benefit shellfish growers through sales channels that Pacific Hybreed has developed. Improved broodstock will be made available to commercial hatcheries through partnerships for larger-scale production to reach more farms and boost locally produced seafood in the U.S.