Special Issue: Genotyping by Sequencing
Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout
Article first published online: 29 OCT 2012
© 2012 John Wiley & Sons Ltd
Special Issue: GENOTYPING BY SEQUENCING IN ECOLOGICAL AND CONSERVATION GENOMICS
Volume 22, Issue 11, pages 3061–3076, June 2013
How to Cite
Hecht, B. C., Campbell, N. R., Holecek, D. E. and Narum, S. R. (2013), Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Molecular Ecology, 22: 3061–3076. doi: 10.1111/mec.12082
- Issue published online: 30 MAY 2013
- Article first published online: 29 OCT 2012
- Manuscript Accepted: 12 SEP 2012
- Manuscript Revised: 5 SEP 2012
- Manuscript Received: 30 JUN 2012
- National Center for Research Resources. Grant Number: 5P20RR016448-10
- National Institute of General Medical Sciences. Grant Number: 8 P20 GM103397-10
- National Institutes of Health
- Bonneville Power Administration. Grant Number: 200900500
Table S1 Polymorphic restriction-site-associated DNA-tag loci detected in this study named after the marker nomenclature of Miller et al. (2012).
Table S2 Complete data set used for genome-wide association study, including life-history classification smolt (1 = smolt, 2 = resident), ATPase [ATPase activity (μmoles/Pi/h/mg Protein)], Sex (1 = male, 2 = female), coefficients of ancestry as inferred by the programs Structure and clumpp (Q1–Q4), and the 11 196 markers R00012–R49475.
Table S3 Results of the eight genome-wide association study analyses run, including linkage group assignment and genetic position in the two linkage maps (Miller_LG, Miller_cM, Miller et al. 2012; Hecht_LG, Hecht_cM, Hecht et al. 2012), Hardy–Weinberg equilibrium (HWE) P-values in Yakima (Yak) and Upper Mann Creek (UMC), genotyping success (%Miss), and minor allele frequency (MAF).
Table S4 Blast2Go results for all 550 restriction-site-associated DNA-tag sequences detected for having a significant association with either the migratory life-history trait or ATPase activity.
Fig. S1 Total raw, quality filtered, and quality filtered and barcode stripped reads from five restriction-site-associated DNA-tag sequencing libraries.
Fig. S2 Histogram of total quality filtered reads for each of 182 fish samples sequenced excluding seven samples with low-yield sequence which were pruned before analyses.
Fig. S3 Rainbow trout restriction-site-associated DNA-tag genetic linkage map adapted from Miller et al. (2012).
|mec12082-sup-0003-FileS1.docx||Word document||17K||File S1 Overview of the steps and commands used in this study for the bioinformatic pipeline of Miller et al. (2012).|
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