Mapping of Quantitative Trait Loci (QTL) Associated with Timing of Metamorphosis from Leptocephali to Glass Eels in Japanese Eel (Anguilla japonica)

Japanese eel (Anguilla japonica) is a valuable economic aquaculture species in East Asia. Eel larvae, called leptocephali, grow much larger than typical fish larvae and have long larval periods. Here, we report on a genome-wide quantitative trait loci (QTLs) scan for timing of metamorphosis from leptocephali to glass eels and several morphological traits of glass eels after metamorphosis by using two-way pseudo-testcross strategy. A total of 287 F₁ offspring derived from a single female and a male phenotyped for timing of metamorphosis  (age at start and end of the metamorphosis), and five morphometric traits. Each 46 offspring metamorphosed in early (metamorphosis were started from 186 to 247 days post hatch (dph)) and late (326 to 447 dph) were selected for QTL mapping. A new linkage map was compiled with 2,672 SNP markers derived from a RAD-seq analysis and 465 SSRs based on the previously published map. QTL mapping was performed with half-sib regression analysis (paternal and maternal) by simple interval mapping. One significant QTL (genome-wide P < 0.05) was found for timing of metamorphosis on linkage group 1 (LG1), and two suggestive QTLs (chromosome-wide P < 0.05) on LG14 and LG16. Three suggestive QTL for body size of glass eels were also found on LG4, LG5, and LG16. The QTL explained between 8% and 15% of phenotypic variance. The results are the first step towards identifying genetic architecture of important traits for mass-production of glass eels in the Japanese eel.