For as long as plants and animals have been domesticated the tendency has been to select species for improvement like better growth, disease resistance, or any character allowing a better yield. Globally, one third of pigs, half of eggs, two thirds of milk and three quarters of broilers are produced with industrial breeding lines. Mariculture genetics is sure to follow, and the trajectory will be steeper with the recent advances in biotechnology and the sequencing of the genome.

The mariculture industry has been slow to adopt quantitative genetics and selective breeding as compared with the plant and farm animal industries. A breeding program for bivalve shellfish would be particularly promising for genetic gains based upon their relatively high fecundity (prolific spawning) and heritability (ability to pass on economically important traits). These factors combined with short generation intervals and recent advances in bivalve shellfish genome sequencing could revolutionize a sustainable and nutritious food source for feeding the future.

Polyploidy is based on changing the number of chromosomes in bivalve shellfish. These polyploids contain the same chromosomes that were present in the eggs. No foreign genes from other species are introduced in this process. This approach has been widely used in the agriculture industry since for example, bananas are triploids, wheat is hexaploidy, blueberries are naturally tetraploid and sugar beets are triploid.

Polyploidy allows the bivalve shellfish industry to produce animals that are sterile. To give birth to the triploid shellfish, no chemicals or genetic engineering are used, rather a tetraploid shellfish, which is bred with four chromosomes and a normal diploid with two chromosomes are then bred to produce a triploid shellfish.

This has many advantages in the culture of bivalve shellfish. Commercially cultivated species expend considerable energy spawning. In a sterile animal this energy is partially redirected to growth. Oysters typically become "soft" or spawny in the summer months making them less desirable for the raw bar trade. Sterile oysters stay firm and full of glycogen year-round. In many growing areas oysters will spawn releasing up to 50% of their body mass and dramatically reduce crop yield for extended periods of time. This problem is averted with a sterile crop. Furthermore, because of their rapid growth, triploids are ready for market before the onset of major mortalities attributed to disease.

Polyploidy refers to a genetic state that can be produced artificially in fish and bivalve shellfish through manipulation of embryos. Polyploidy is highly regarded in China and has been studied in close to 30 shellfish species, including Pacific oysters, scallops, and abalone. Thanks to extensive research efforts in the field of polyploidy, triploid oyster breeding has developed into an industry in coastal China, with triploid oysters exhibiting increased flesh quality and growth compared to diploids: triploid Pacific oysters are 17% larger than diploids prior to spawning and more than 30% larger after spawning.

Besides advantages such as increased growth rates, use of sterile triploids in mariculture can help protect the genetic diversity of native populations and prevent establishment of populations of escaped organisms. Tetraploids are induced in a similar way as triploids, but during a more advanced stage of embryonic development. A tetraploid/diploid cross would be expected to produce all-triploid progeny that might be more viable than mechanically induced triploids, as triploid embryos would not have to undergo the same stress and damage that occurs during mechanical induction.

Molecular biologists bring laboratory-based approaches about the workings of genes, proteins, chromosomes and cells. Computational biologists focus on the design and development of algorithms that analyze DNA, protein sequences and other biological data. The science is based on principles that have been developed over thousands of years with plants and farmed animals and now accelerated by digital technologies. There is no genetic engineering; only the adaption of recent scientific short cuts for eliminating undesired genetic characteristics rather than breeding for desired traits.

Advanced molecular and computational technologies take a unique approach for reducing the lengthy and tedious selective breeding process. For example, with traditional selective breeding programs, the largest and fastest growing bivalve shellfish families are bred with other families to influence the basic genetics revealing specific DNA sequences in the majority of that population. With this data, scientists evaluate generic bivalve shellfish DNA to better understand specific sequence changes for elucidation with genetic sweeps by powerful computers. By understanding the variations in DNA that cause good traits scientists skip, or reduce, the expensive and time-consuming trial and error of traditional breeding for producing a product that has all or most of the desired traits.

Here’s how it works: DNA gets coded into RNA, which is made into proteins for producing an organism. RNAi interferes (hence the 'i') with any unwanted RNA sequence by silencing implicated genes. By removing a piece of RNA that is essential for life, the organism dies resulting in dead shellfish larvae. Reagent companies sell “virtual kits” consisting of complex, proprietary algorithms to predict sophisticated sequences. By targeting variations in RNA not wanted in each organism and adding programmed RNAi chemical reagents into a tank containing millions of larvae those that are unwanted become mortalities. The surviving larvae would have the exact type of RNA with the prescribed suite of traits. Using this technique eliminates the requirement of sequencing each generation. It's basically a scientific short-cut for a genetic filtering process using the same principle that natural selection has employed over eons.

This technique provides an exciting opportunity for the advancement of science and global food security and a novel way to quickly produce a bivalve shellfish species with selected features of economic interest by mimicking natural selection. Because RNAi is not heritable, subsequent bumper crops can be harvested without the GMO stigma. This expertise is transferrable to the selective breeding of other broadcast-spawning bivalves for delivering gains by shortening growth cycles, improving yields, and increasing uniformity. There is also the potential for breeding for specific, high-value markets requiring consistency in size, shape, coloration, and greater Omega-3 content. Cutting-edge molecular and computational technologies promise an economic breakthrough for the global sustainable bivalve shellfish industry.