Marine Biotechnology

, Volume 16, Issue 3, pp 289–298

Molecular Markers for Variation in Spawning Date in a Hatchery Population of Rainbow Trout (Oncorhynchus mykiss)

Original Article

DOI: 10.1007/s10126-013-9547-7

Cite this article as:
Allen, M.S., Ferguson, M.M. & Danzmann, R.G. Mar Biotechnol (2014) 16: 289. doi:10.1007/s10126-013-9547-7


We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker–trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76 %. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date.


Life historyCircadian genesMarker–trait associationsSalmonid fishes

Supplementary material

10126_2013_9547_MOESM1_ESM.pdf (42 kb)
Supplementary File 1Bonferonni Hardy-Weinberg equilibrium (HWE) tests for all 63 loci shown with p-values and standard error. Asterisk show which loci remain out of HWE after correction. (PDF 41 kb)
10126_2013_9547_MOESM2_ESM.pdf (27 kb)
Supplementary File 2Delta K (ΔK) plot showing the number of subpopulations (K) on the x-axis and the calculated ΔK values on the y-axis. The large spike at K=2 indicates that this is the most likely value of K. (PDF 27 kb)
10126_2013_9547_MOESM3_ESM.pdf (101 kb)
Supplementary File 3Possible candidate genes for marker-trait associations on RT-23 based upon synteny homologies with medaka chromosome 17. (PDF 101 kb)
10126_2013_9547_MOESM4_ESM.pdf (168 kb)
Supplementary File 4Possible candidate genes for marker-trait associations on RT-12 based upon synteny homologies with medaka chromosome 5. (PDF 167 kb)

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • M. S. Allen
    • 1
  • M. M. Ferguson
    • 1
  • R. G. Danzmann
    • 1
  1. 1.Department of Integrative BiologyUniversity of GuelphGuelphCanada