NOAA 'Omics Seminar Series: Understanding the genetic basis of run timing diversity in salmon

Date: November 20, 2024
Title: Understanding the genetic basis of run timing diversity in four species of Pacific salmon
Presenter: Wes Larson
Abstract: Migration is an important component of the life cycles of many organisms and differences in migration timing can greatly influence fitness. Variation in migration timing (hereafter referred to as run timing) is found in many salmon species and contributes to the portfolio of life history diversity that is vital for maintaining healthy populations. Large effect loci that strongly influence run timing have been discovered in Chinook salmon and steelhead and these loci have been a major focus of research and conservation efforts over the last decade. However, the genetic basis of run timing variation has not been investigated in other Pacific salmon. Here, we use a combination of whole genome sequencing and targeted amplicon sequencing to identify loci associated with run timing variation in sockeye, pink, chum, and coho salmon. We find that two small genomic regions on homeologous chromosomes that arose after an ancient whole genome duplication are strongly associated with run timing across the four species. The genes most closely associated with these regions are the Leucine Rich Repeat Containing 9 (LRRC9) gene and the Estrogen Receptor Beta (ESRB) gene. The LRRC9 region is associated with run timing in sockeye, chum, and pink salmon, and the ESRB region is associated with run timing in chum and coho salmon. Notably, the Six6 gene, which is associated with age-at-maturity in steelhead and Atlantic salmon, is also found near the regions we identified. Our results suggest that the two duplicated versions of this region are highly associated with variation at multiple phenotypes in salmon. We hypothesize that this may be a master regulatory region that influences gene expression at many genes involved in multiple physiological pathways. Knowledge of patterns of variation at this major affect locus can be leveraged to help maintain the evolutionary potential of salmon populations and understand how they may respond to future stressors.