Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)

Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine
are managed as a single stock despite several lines of evidence supporting
two spawning groups (spring and winter) that overlap spatially, while
exhibiting seasonal spawning isolation. Low-coverage whole genome
sequencing was used to evaluate the genomic population structure of
Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank
using 222 individuals collected over multiple years. Results indicated low
total genomic differentiation, while also showing strong differentiation
between spring and winter spawning groups at specific regions of the
genome. Guided regularized random forest and ranked F­ST methods were used
to select panels of single nucleotide polymorphisms (SNPs) that could
reliably distinguish spring and winter-spawning Atlantic cod (88.5%
assignment rate), as well as males and females (95.0% assignment rate)
collected in the western Gulf of Maine. These SNP panels represent a
valuable tool for fisheries research and management of Atlantic cod in the
western Gulf of Maine that will aid investigations of stock production and
support accuracy of future assessments.