Mapping QTL for cold-tolerance trait in a GIFT-derived tilapia line by ddRAD-seq

Tilapia is an economically important fish in the world. High mortality caused by low temperature is a serious problem to tilapia farming during overwintering. In this study, a genome-wide significant QTL interval, located on chrLG18, controlling cold-tolerance trait was identified in a full-sib family of GIFT originated tilapia line using ddRAD-seq-based QTL mapping. The QTL explained 21.5% of phenotypic variances. Six pairs of microsatellite markers were successfully developed within this interval. For the microsatellite marker SSR613719, which had two genotypes in the population, ‘lm’ and ‘ll’, the number of individuals with the ‘ll’ genotype was significantly higher than the number of individuals with the ‘lm’ genotype in the cold sensitive population ( p < 0.05). This independent test indicated the reliability of the detected QTLs. The expression of candidate genes ( pak1ip1 , loc100696456 and loc100697261 ) in the QTL interval was significantly affected under cold treatment as indicated by qRT-PCR test. This study provides important information for marker-assisted selection of cold tolerant tilapia lines. • A QTL interval on chrLG18 associated with cold tolerance was identified in tilapia. • Nine candidate genes in this QTL were found differentially expressed exposed to cold stress. • Six microsatellite markers were significantly associated to cold-tolerance trait.