Table 7 Predicted changes to the amino acid sequence based on cDNA alignments of genes within metabolism-related QTL that display evidence of non-neutral evolution by HapFLK analysis and have fixed differences between RÃo Choy surface fish and Pachón cavefish (n = 10 fish per population)
Trait | Gene name | Predicted surface to Pachón amino acid changes |
|---|---|---|
Blood glucose | adam9 | F87L, T255Ffs*, Q384R, D553E, K681N |
Weight and length | ano5b | K67E*, S119L, K639R |
Weight and length | dpep2 | No gene annotated in surface fish genome |
Body condition | ahnak2 | E104K* |
Body condition | exoc3l4 | K431R*, L435M, L483S*, H524Q*, L527E |
Gonad weight | amfr | Two synonymous differences |
Gonad weight | ano9a | L42W*, E178D*, E362D, T735I*, A811G*, L744Q*, P749H, V752F*, G757S*, E835K |
Gonad weight | cd44a | I9M*, Y23_F34del*, Q53_L54insRSCARFWVQHWPV* |
Gonad weight | slc1a2b | Q215E |
Gonad weight | ENSAMXG00000016170 | No gene annotated in surface fish genome |
Gonad weight | gzm3 | V28A*, R33L*, E131V, D175S, S196A, T201S, K204T, K216Q*, L226G, T227F |
Gonad weight | si:dkey-100n23.5 | R184del* |
Gonad weight | tnfsf13b | One synonymous difference |
Liver size | si:ch1073-174d20.1 | A9V, S101N |
Liver size | nfat5a | D43A, T550N, N611K, Q918K, N1079_Q1083del*, Q1084E*, T1093S, S1293A, I1334M |
Hindgut length | cbf2 | Y389H*, M542T* |
Hindgut length | cbf1 | R27T*, R46Q*, S48P*, V75A*, F101Y*, H142D, E264Q, M266I, K299N, T387I*, E561D, I621N*, K671T* |
Hindgut length | zgc:110782 | E92K |
Hindgut length | gpr119 | No gene annotated for surface fish genome |
Hindgut length | rbm14a | Two synonymous differences |
Hindgut length | rin1a | S203N, M464Q*, G768S |
Hindgut length | mark2a | S392N*, N722K |
Hindgut length | adssl | F108Lfs*, N224Y, K338R, N367Tfs*, A404Lfs*, C444R |
Hindgut length | spry3 | P3L |
Hindgut length | rce1b | P116S, I147Lfs*#, F193del*# |
Hindgut length | tenm2 | W411Ffs* |
Hindgut length | zgc:77262 | G288_A291del*, P293_P294del*, G327S |
Hindgut length | lsm14b | G78C*, A173T*, L266S* |
Hindgut length | fam65b/ripor2 | D468Efs*#, R664H |
Hindgut length | rfx5 | G342R* |
Hindgut length | txnla | A496T, E504K*, F529C* |
Hindgut length | cpsf1 | L53P*, E355D*, A702T* |
Hindgut length | adck5 | M552I, A569V* |