Lack of genetic information is a hurdle to implementing an effective and efficient selective breeding program in many aquaculture species . The examination of genome-wide variable sites within a species allows for the identification of genes which are associated with desirable traits for aquaculture, such as increased growth rate and decreased inbreeding . Once identified, these genes can be positively selected for in a genetics based selective breeding program . Restriction site-associated DNA sequencing (RADSeq) is a quick and cost-efficient sequencing method used in genome-wide genotyping studies. 2b-RAD sequencing , a type of RADSeq, uses a type IIB restriction endonuclease to cut the genome into small, equally sized DNA fragments that can be sequenced faster than whole-genome sequencing. It allows for higher power with a smaller number of samples when conducting high throughput genotyping in populations.
The Florida Pompano (Trachinotus carolinus ) is a warm-water, marine teleost species found in the Atlantic Ocean off the coast of Massachusetts, U.S. down to Brazil. It is commonly found off the east and west coasts of Florida, U.S. where it is known as a popular food fish. There is great interest in bringing this species to large scale aquaculture due to its popularity and high market value. A genetics-based selective breeding program would allow for increased production rates in an aquacultural setting resulting in greater profits for farmers . An assessment of the genetic variability of the wild Florida Pompano populations is necessary to select the best candidates to include in a selective breeding program (broodstock).
Towards this end, this project genotyped n=30 Florida Pompano caught off the east coast of Florida . Total genomic DNA was extracted from fin clips. Genomic libraries were prepared following the 2b-RAD sequencing protocol and sequenced on Illumina HiSeq 3000 platform . Sequenced reads were filtered for low-qualit y and uninformative reads and mapped using a Florida Pompano reference genome developed by our team. Multi-loci genotypes are being analyzed to estimate levels of genetic variation in the wild population. This information will lay the foundation to identify genes of interest that can be used in a genetics-based selective breeding program for enhanced seedstock.