Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

Abstract

To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using non-parametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1 % of the genome-wide significance and accounted for 14.6–18.9 and 14.7–18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s10126-015-9673-5) contains supplementary material, which is available to authorized users.

Quantitative trait locus mapping of growth‐related traits in inter‐specific F 1 hybrid grouper ( Epinephelus fuscoguttatus × E. lanceolatus ) in a tropical climate

“…It is common to find a difference in the recombination rate between two sexes in any fish species, as female map distances are usually larger than those of males. Female:male recombination ratios of 1.03:1, 1.12:1 and 1.19:1 have been reported for orange‐spotted, kelp and white groupers, respectively (Dor et al., ; Kessuwan et al., ; You et al., ). In this study, segregating alleles in progeny from the dam and sire were used to construct the tiger grouper and giant grouper linkage maps respectively.…”

“…However, because of the very long period for sexual maturation and gonadal development (at least 6 years in this hybrid grouper; Luin, Fui & Senoo, ), >10 years are needed to establish F 2 populations. Growth‐related QTLs have been successfully detected in several fish species using F 1 families (Kessuwan et al., ; Song et al., ; Wang et al., ). We used F 1 populations to construct linkage maps with codominant molecular markers and performed a QTL analysis although F 1 families are usually not as efficient for mapping QTLs compared with F 2 populations (Doerge, ).…”

“…Where possible, SSR markers were chosen at 20 centimorgan (cM) intervals to ensure adequate QTL detection power (Massault, Bovenhuis, Haley & Koning, ) and comprehensive coverage of the genome. When markers selected from the previous kelp grouper map (Kessuwan et al., ) were not polymorphic, other markers found at a nearby location on the same linkage group in the tiger grouper map (Kessuwan personal communication) were selected. In total, 399 SSR markers including 103 newly developed markers were used in this study.…”

“…Graphic representations of the linkage groups were generated using MapChart version 2.1 (Voorrips, ) using the raw recombination fractions as map distance estimates. A linkage group number was assigned based on the kelp grouper map (Kessuwan et al., ). The estimated genome lengths ( Ge ) of the tiger grouper and giant grouper genomes were calculated using two different methods as reported previously by Song et al.…”

“…Quantitative trait locus (QTL) mapping is an effective way to identify the genomic regions responsible for variations in complex traits, including growth‐related traits (Liu & Cordes, ). Several studies on QTLs affecting growth‐related traits have been carried out in salmonids (Moghadam et al., ; Wringe et al., ), sea bass (Wang, Wan et al., ), tilapia (Liu et al., ), common carp (Wang, He, Ma & Wang, ), Japanese flounder (Song et al., ), gilthead sea bream (Loukovitis et al., ), turbot (Wang, Hu et al., ) and kelp grouper (Kessuwan et al., ). Growth‐related traits are generally associated with multiple genes that have small effects across the genome and are determined using the combined forces of genetic and environmental factors and their interactions (Mackay, ).…”