Hatchery International

Features Genetics Research
SNP’s Vs. Microsatellites: Out with the old and in with the nucleotides

October 2, 2023  Sponsored by The Center for Aquaculture Technologies

Bob Dylan once said, “the times, they are a-changin’”, and this sentiment rings as true today as the day it was written. For those who embrace change, the future is bright, and this is certainly true in the realm of genotyping. Over the past 154 years, researchers have progressed from the identification of DNA to the widespread use of genotyping as a foundational tool in aquaculture breeding, management, and research. Like the times, genotyping methodology has changed as well. The old and established practice was based on the use of microsatellites, which works well for some limited applications. However, those companies interested in receiving the highest quality information, in a customized fashion, and with less expense, are using SNPs (single nucleotide polymorphisms) as their genotyping tool. The question companies interested in genotyping must ask themselves is this: are we stuck in the past or will we embrace the future?

To understand the benefits of SNPs over microsatellites, it’s important to understand these two genotyping methods. Microsatellites look at parts of the genome which have repeating nucleotide sequences. From there, users can identify differences between individuals or groups by looking for small differences within those repeated parts of the genome and building statistical associations. A SNP is a single nucleotide difference, and these are scattered throughout the genome. Using SNPs means targeting and identifying specific nucleotide locations in the genome, including locations within genes associated with certain characteristics, seeing which nucleotide occupies that location, interpreting that data, and generating statistically useful information. Here are the advantages of SNPs compared to microsatellites:

1. Broader Genomic Coverage: SNP arrays cover a much larger portion of the genome compared to microsatellites, providing more comprehensive information about an individual’s genetic makeup. This broader coverage enables researchers and breeders to access a wealth of genetic data, leading to a deeper understanding of genetic diversity, relatedness, and population structure. SNP arrays can be classified by how many locations in the genome they cover and are labeled as low density, medium density, or high density. 

Low-density arrays have less than 1,000 SNPs and can be used to explain the genetic structure of the population, including understanding diversity, relatedness, and levels of inbreeding. They are also useful for parentage assignment and can be customized to include tests for genetic sex, species identification, or geographic origin. Microsatellites can be used reasonably well for these same applications. Medium-density arrays include up to 10,000 SNPs and can be used to increase precision, impute to high-density information for genomic selection, and expand low-density applications. High-density arrays boast over 10,000 SNPs, enabling their utilization in various cutting-edge applications. From in-depth parentage and marker-assisted selection to genomic selection and genome-wide association studies (GWAS), they diligently identify markers linked to genomic regions associated with performance traits, genetic variation and inbreeding assessment. These techniques are very difficult with microsatellites; thus, SNPs are required to conduct cutting-edge genetic research.


2. Higher Precision and Resolution: SNPs stand out for their elevated precision and resolution, surpassing microsatellites. While microsatellites are used to analyze genome regions with repetitive DNA sequences, SNPs target specific individual nucleotide variations across the full genome. This targeted approach allows for more accurate identification of genetic differences and associations with particular traits or characteristics.

3. Automated Data Collection and Analysis: SNPs are much easier to identify compared to microsatellites. SNP genotyping brings the benefits of automation and standardization in data collection and analysis, streamlining the entire genotyping process. This automation significantly reduces the time and resources required to process large numbers of samples or large numbers of markers, making SNPs ideal for high-throughput applications and data analysis.

4. Highly Customizable Assays: SNP arrays are highly customizable, allowing researchers and companies to design arrays tailored to their specific species, populations, research goals, or breeding objectives. This flexibility enables the inclusion of markers associated with particular performance traits, diseases, or environmental adaptation. In contrast, Microsatellites are difficult to identify, and customization after creating a panel is a significant amount of work.

5. Cost-Effectiveness and Scalability: Contrary to misconceptions, SNP genotyping is typically more cost-effective than microsatellites due to advantages in automation and scalability, and the relative ease at which customization of SNP panels is possible. The ability to process large quantities of samples simultaneously reduces per-sample costs, making SNP arrays a cost-efficient choice for large-scale projects.

6. Future-Ready Technology: The widespread adoption of SNPs lays the foundation for future advancements in genotyping technology. The wealth of actionable data generated by SNP arrays contributes to the development of new applications, analyses, and technologies. With every new genome sequenced, additional SNPs are mapped and available to be used in genotyping applications. Another benefit of widespread SNP adoption is that genotyping technology is always improving and evolving. SNPs remain a key part of this evolution, and actionable SNP data will feed into new applications and a next generation of analyses and technologies. Ultimately, this advancement will enable analyses with millions of SNPs at a time. Importantly, evolving SNP technologies now facilitate the identification of actual DNA changes in genes linked to desirable traits, opening the door to genome editing for aquaculture. Genome editing, as a developing technology, holds the promising potential to revolutionize aquaculture selective breeding in the very near future.

As leaders in genetic research, the Center for Aquaculture Technologies has extensive experience in the use of both microsatellites and SNPs. With very few exceptions, we advise clients to switch to using SNPs if they have not already, owing to the clear and extensive benefits outlined above. On the benefits of SNPs, Jason Stannard, CAT’s Director of Genotyping, says, “not only have SNP tools and technologies increased and improved, but the cost to run a given sample has dropped dramatically.”

In summary, SNP genotyping offers superior precision, broader genomic coverage, automated data processing, and high customizability. Contrary to the notion of being more expensive, SNPs provide cost-effective solutions for large-scale genotyping projects. Moreover, their implementation sets the stage for the future of genetic research and applications in aquaculture and beyond. Embracing SNP technology allows researchers and companies to stay at the forefront of genomics, harnessing its potential to drive advancements in aquaculture breeding, management, and research. With SNPs, organizations in the industry can unlock the ability to gather vast data and transform it into invaluable insights quickly and affordably. The times are changing, and so is genotyping. Embrace the future and make the switch!

To learn more about The Center for Aquaculture Technologies (CAT), visit aquatechcenter.com.

Print this page


Stories continue below