QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.)

Mar Biotechnol (NY). 2019 Jun;21(3):384-395. doi: 10.1007/s10126-019-09888-9. Epub 2019 Mar 12.


Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.

Keywords: Body color; MAS; QTL; Red blotches; Red tilapia; ddRAD-seq.

MeSH terms

  • Animals
  • Aquaculture
  • Breeding
  • Genome-Wide Association Study
  • Phenotype
  • Pigmentation / genetics*
  • Quantitative Trait Loci / genetics*
  • Tilapia / genetics*