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. Author manuscript; available in PMC: 2011 Apr 1.
Published in final edited form as: J Evol Biol. 2010 Mar 1;23(4):840–853. doi: 10.1111/j.1420-9101.2010.01954.x

Table 4.

Test for single marker association between markers at the opsins or elsewhere in the genome and gene expression for each opsin. Linkage group (and position in cM) is taken from the tilapia map (Lee et al 2005). The relative marker positions on LG4 are taken from the mbuna map of Albertson et al 2003 relative to the known position of UNH911 on the tilapia map. For each marker, we list the number of individuals that were successfully genotyped, the degrees of freedom for the F statistic, and then for each gene we list the F statistic and p value. Markers which are statistically significant after sequential Bonferroni correction are shown in bold. (p values are given in Supplementary Table 1).

A. DC cross:
Marker Linkage group
(cM)		 # ind genotyped d.f. F statistic ** p<0.01
fSWS1 fSWS2B fSWS2A fRH2B fRH2A fLWS
Green opsin 5 (18) 26 3, 22 0.699 0.658 0.789 0.750 1.392 0.084
Red-blue opsin 5 (48) 29 2, 26 0.066 0.070 1.160 0.628 0.524 0.502
UV opsin 17 28 2, 25 0.549 0.610 0.113 0.009 2.394 0.631
UNH2008 2 28 2, 25 1.769 1.627 2.935 1.099 1.986 0.403
UNH2016 4 (16) 31 2, 28 0.061 0.046 0.530 0.746 1.461 0.340
UNH2126 4 (19) 29 2, 26 0.481 1.250 3.004 0.627 5.988 3.092
UNH2156 4 (20) 31 2, 28 0.013 0.015 0.424 0.748 7.152** 4.274
UNH911 4 (22) NS
UNH2003 6 29 2, 26 0.400 0.411 0.094 0.051 0.815 0.055
UNH2164 6 31 2, 28 0.015 0.090 1.237 0.442 0.943 1.332
UNH2153 7 32 1, 30 1.267 1.097 0.867 0.088 0.005 0.060
UNH129 8 32 3, 28 2.073 2.020 2.396 2.143 0.849 1.541
UNH875 9 29 2, 26 0.001 0.008 0.683 0.080 0.087 0.010
UNH2084 12 32 2, 29 1.715 1.579 2.728 1.878 0.204 2.572
UNH934 13 (10) 31 3, 27 0.525 0.393 1.046 0.610 0.118 0.381
GM373 13 (20) 31 1, 29 0.909 0.699 1.209 0.724 0.004 0.722
UNH173 13 (22) NA
GM641 13 (25) 32 2, 29 4.342 3.800 3.460 2.340 0.436 1.684
UNH997 13 (31) NV
GM262 13 (32) 32 1, 30 1.033 0.724 2.033 2.307 0.920 0.800
GM507 13 (32) 30 2, 27 0.916 0.883 0.823 0.916 1.969 2.056
UNH954 13 (32) NV
GM686 13 (33) 28 1, 26 4.779 5.527 0.047 2.574 0.320 1.405
UNH1008 13 (34) NA
GM299 13 (39) NV
UNH871 13 (41) 29 2, 26 3.883 3.041 3.703 3.293 0.288 3.587
UNH2166 15 30 3, 27 0.274 0.316 0.638 1.468 0.955 3.072
NA = no amplification
NS = not scorable
NV = not variable in cross
B. TA cross
Marker Linkage group
(cM)		 # ind genotyped d.f. F statistic *p<0.05; ** p<0.01
SWS2B SWS2A RH2B RH2A LWS
Green opsin 5 47 2, 44 0.500 0.439 3.901 0.633 0.614
Red-blue opsin 5 47 2, 44 4.637 4.756 5.503* 2.033 0.529
UV opsin 17 44 2, 41 1.644 1.729 1.182 0.021 0.063
UNH2156 4 45 2, 42 0.244 0.245 0.504 0.838 1.099
GM373 13 (2) NS 2, 44
GM641 13 (25) 47 2, 44 6.415** 6.338** 0.750 0.415 0.766
GM262 13 (32) NV
GM507 13 (32) 47 2, 44 6.998** 7.520** 0.986 1.299 0.765
GM686 13 (33) NA
GM299 13 (39) NS
UNH871 13 (41) 47 2, 44 7.638** 7.666** 0.354 0.846 0.999

NA = no amplification

NV = no variation

NS = not scorable