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 F 1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using nonparametric 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 genomewide 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.

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp ( Hypophthalmichehys nobilis )

“…In recent years, a number of high-density genetic linkage maps have been constructed in aquaculture species based on microsatellites, such as Asian seabass (790 SSRs) (Wang et al, 2011a), Atlantic salmon (1179 SSRs) (Danzmann et al, 2008), Japanese flounder (1487 SSRs) (Song et al, 2012b), half-smooth tongue sole (1007 SSRs) (Song et al, 2012a), silver carp (703 SSRs) (Guo et al, 2013b) and kelp grouper (714 SSRs) (Kessuwan et al, 2015). In this study, a new genetic linkage map of bighead carp was constructed based on 905 SSRs, with an average marker interval of 1.8 cM which was slightly lower than Japanese flounder (1.35 cM) and half-smooth tongue sole (1.67 cM), but higher than other three maps mentioned above (2.2 cM-4.1 cM).…”

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

“…SSRs are short, tandemly repeating nucleotide motifs (1–6 bp long) that are widely distributed in genomes of eukaryotic organisms genomes including flax (Tautz, 1989; Temnykh et al, 2001). The abundance, highly polymorphic nature, heritability, distribution, reproducibility and generally co-dominant nature of SSR markers make them highly suitable for MAS and genetic diversity studies (Wiesner et al, 2001; Cloutier et al, 2011, 2012b; Soto-Cerda et al, 2011a; Kumar et al, 2015; Kessuwan et al, 2016). …”

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

“…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, 2014;Kessuwan et al, 2016;You et al, 2013). 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.…”

“…An additional analysis with adequate detection power using more markers will be required to confirm this epistatic QTL. QTLs detected on Efu_LG10, 13 and 19 with a relatively higher LOD score on the tiger grouper map and the QTL located on Ela_LG3 on the giant grouper map of family A were not detected in family B. However,Kessuwan et al (2016) reported major or putative QTLs for body weight or total length on linkage groups EBR8, 10, 13 and 19 in kelp grouper. The linkage groups EBR8, 10, 13 and 19 on the kelp grouper map were equivalent to the linkage group Efu_LG8, 10, 13 and 19 and Ela_LG8, 10, 13 and 19 on the tiger and giant grouper maps respectively.…”

“…Where possible, SSR markers were chosen at 20 centimorgan (cM) intervals to ensure adequate QTL detection power (Massault, Bovenhuis, Haley & Koning, 2008) and comprehensive coverage of the genome. When markers selected from the previous kelp grouper map (Kessuwan et al, 2016) 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.…”