Isolation and inheritance of novel microsatellites in Chinook Salmon (Oncorhynchus tschawytscha)

We describe the isolation, PCR amplification, and characterization of 10 new microsatellite loci (Ots-1–Ots-10) for the federally protected chinook salmon (Oncorhynchus tschawytscha). We investigate the inheritance and linkage of these loci as well as a previously published locus, Onem13, in families obtained from artificial crosses. Mendelian transmission is confirmed for 76 of 80 segregations observed. Of the four deviations, two appear to have resulted from gametic segregation distortion. The other two provide evidence for the existence of at least one null allele. We also identify ‘‘drop out’’ of large alleles in these two families owing to competitive PCR amplification of smaller alleles. There is no evidence for linkage between any pair of loci. One mutation observed at Ots-2 is reported and confirmed by DNA sequencing. We estimate the mutation rate at this locus to be 6.5 3 10–4 (95% confidence interval 3.6 3 10–3 to 1.6 3 10–4, respectively). Characterizing a mutant allele at Ots-2 offers the first step toward understanding mutation rates for chinook microsatellites. Owing to their Mendelian inheritance, these new loci provide reliable markers for high-resolution population genetics studies of this species.