Marine Biotechnology

, Volume 10, Issue 5, pp 579–592

Determination of Quantitative Trait Loci (QTL) for Early Maturation in Rainbow Trout (Oncorhynchus mykiss)

  • Lisa Haidle
  • Jennifer E. Janssen
  • Karim Gharbi
  • Hooman K. Moghadam
  • Moira M. Ferguson
  • Roy G. Danzmann
Original Article

DOI: 10.1007/s10126-008-9098-5

Cite this article as:
Haidle, L., Janssen, J.E., Gharbi, K. et al. Mar Biotechnol (2008) 10: 579. doi:10.1007/s10126-008-9098-5

Abstract

To identify quantitative trait loci (QTL) influencing early maturation (EM) in rainbow trout (Oncorhynchus mykiss), a genome scan was performed using 100 microsatellite loci across 29 linkage groups. Six inter-strain paternal half-sib families using three inter-strain F1 brothers (approximately 50 progeny in each family) derived from two strains that differ in the propensity for EM were used in the study. Alleles derived from both parental sources were observed to contribute to the expression of EM in the progeny of the brothers. Four genome-wide significant QTL regions (i.e., RT-8, -17, -24, and -30) were observed. EM QTL detected on RT-8 and -24 demonstrated significant and suggestive QTL effects in both male and female progeny. Furthermore, within both male and female full-sib groupings, QTL on RT-8 and -24 were detected in two or more of the five parents used. Significant genome-wide and several strong chromosome-wide QTL for EM localized to different regions in males and females, suggesting some sex-specific control. Namely, QTL detected on RT-13, -15, -21, and -30 were associated with EM only in females, and those on RT-3, -17, and -19 were associated with EM only in males. Within the QTL regions identified, a comparison of syntenic EST markers from the rainbow trout linkage map with the zebrafish (Danio rerio) genome identified several putative candidate genes that may influence EM.

Keywords

QTLEarly maturationSalmonidsLife history

Supplementary material

10126_2008_9098_Fig1a_ESM.gif (234 kb)
Supplementary Fig. 1

Scanone R/qtl plots obtained from the EM likelihood analysis of the early maturation binary trait data. Markers are arrayed left to right within their respective linkage groups, but marker orders may differ across parents. Analyses were performed for female and male progeny separately for each parent. Genome-wide significance levels are shown by red and green dashed lines while the approximate chromosome-wide significance level is indicated with blue-dashed line (GIF 234 kb), (GIF 129 kb), (GIF 179 kb), (GIF 163 kb), (GIF 175 kb)

10126_2008_9098_Fig1b_ESM.gif (129 kb)
Supplementary Fig. 1

Scanone R/qtl plots obtained from the EM likelihood analysis of the early maturation binary trait data. Markers are arrayed left to right within their respective linkage groups, but marker orders may differ across parents. Analyses were performed for female and male progeny separately for each parent. Genome-wide significance levels are shown by red and green dashed lines while the approximate chromosome-wide significance level is indicated with blue-dashed line (GIF 234 kb), (GIF 129 kb), (GIF 179 kb), (GIF 163 kb), (GIF 175 kb)

10126_2008_9098_Fig1c_ESM.gif (180 kb)
Supplementary Fig. 1

Scanone R/qtl plots obtained from the EM likelihood analysis of the early maturation binary trait data. Markers are arrayed left to right within their respective linkage groups, but marker orders may differ across parents. Analyses were performed for female and male progeny separately for each parent. Genome-wide significance levels are shown by red and green dashed lines while the approximate chromosome-wide significance level is indicated with blue-dashed line (GIF 234 kb), (GIF 129 kb), (GIF 179 kb), (GIF 163 kb), (GIF 175 kb)

10126_2008_9098_Fig1d_ESM.gif (163 kb)
Supplementary Fig. 1

Scanone R/qtl plots obtained from the EM likelihood analysis of the early maturation binary trait data. Markers are arrayed left to right within their respective linkage groups, but marker orders may differ across parents. Analyses were performed for female and male progeny separately for each parent. Genome-wide significance levels are shown by red and green dashed lines while the approximate chromosome-wide significance level is indicated with blue-dashed line (GIF 234 kb), (GIF 129 kb), (GIF 179 kb), (GIF 163 kb), (GIF 175 kb)

10126_2008_9098_Fig1e_ESM.gif (175 kb)
Supplementary Fig. 1

Scanone R/qtl plots obtained from the EM likelihood analysis of the early maturation binary trait data. Markers are arrayed left to right within their respective linkage groups, but marker orders may differ across parents. Analyses were performed for female and male progeny separately for each parent. Genome-wide significance levels are shown by red and green dashed lines while the approximate chromosome-wide significance level is indicated with blue-dashed line (GIF 234 kb), (GIF 129 kb), (GIF 179 kb), (GIF 163 kb), (GIF 175 kb)

10126_2008_9098_Fig2_ESM.gif (127 kb)
Supplementary Fig. 2

TAMRA-labelled DNA fragments generated for the various EM QTL markers detected in rainbow trout. Associations of marker to linkage groups are indicated by the solid black bar at the top of each set of markers. For each panel, the maternal parent (93-32-3) and paternal parent (94-37-8) of family 96-7-C are shown in the left and rightmost lane, respectively. One of the three full-sib brothers (i.e., 96-7-C4) is shown in the middle lane. Allele sizes (bp) for both of the parents and their three male offspring are given in Table 5. The smallest allele bp sizes are at the bottom of the panel and increase in size in ascending order within each figure. Panels are not represented to a uniform scale (GIF 126 kb)

10126_2008_9098_Fig3_ESM.gif (149 kb)
Supplementary Fig. 3

Scantwo R/qtl plots from linkage group RT-8 depicting combined male- and female-specific QTL regions using sex as a co-variate. Epistasis LOD peaks are shown in the upper left of the figure according to the left-hand side of the LOD scale depicted. Additive LOD scores are shown in the lower right with the highest LOD peak (3.678) according to the right-hand side of the LOD scale depicted. The highest LOD score quadrant indicates that two contributing regions (OmyFGT12TUF and OMM1304) are likely present in the genome of this female (GIF 149 kb)

Copyright information

© The Author(s) 2008

Authors and Affiliations

  • Lisa Haidle
    • 1
  • Jennifer E. Janssen
    • 1
  • Karim Gharbi
    • 1
    • 2
  • Hooman K. Moghadam
    • 1
  • Moira M. Ferguson
    • 1
  • Roy G. Danzmann
    • 1
  1. 1.Department of Integrative BiologyUniversity of GuelphGuelphCanada
  2. 2.Institute of Comparative MedicineUniversity of GlasgowGlasgowUK