Genetic markers can be used for population genetic studies as they can help distinguish between individuals and determine genetic variation and relatedness within and between populations. Until now, the number of published genetic markers for the black bear is very limited and only tested in a few small populations. In addition, it is unknown whether they segregate independently or if they are linked and thereby decreasing their usefulness.
Among the most used markers in genetic studies are the Simple Sequence Length Polymorphism (SSLP) or microsatellite markers and the Single Nucleotide Polymorphism (SNP) markers. Our recent studies, in which we sequenced the complete genome of several black bears from Maine and Alaska, allow for the extraction of information on SSLP and SNP markers that can be used for future genetic studies.
We provide this information freely and without restrictions in the hope that it will assist others with their studies.
Developing new SSLP markers is a tedious process in which primers need to be developed spanning the SSLP sequence, tested for PCR amplification, and tested for genetic variation within the population to be studied. Only about a dozen SSLP markers have been published so far for the black bear.
Using our black bear genome sequence (Srivastava, 2019), Juan Manuel Cabrera (Universidad Nacional del Litoral, Santa Fe, Argentina) has done the first step in this process using the program FullSSR (Metz et al 2016). He developed primer pairs for the amplification of 111,495 CA-repeats, the most common SSLP in the genome. Primer sequences and details can be found here: SSLP markers
With the available black bear genome sequence and FullSSR program it is relatively easy to develop primers for other types of repeats. If you do, please let us know and add the information to our database so others can benefit.
After sequencing the genome from a single male black bear from Maine at a x coverage, we also sequenced 4 Maine and 4 Alaskan black bears at a 5x coverage to develop SNP markers. We identified a total of 3,738,117 SNPs among these 8 animals. Details on these SNPs markers can be found here: LINK