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

Abstract

Growth‐related traits are the main target of genetic breeding programmes in grouper aquaculture. We constructed genetic linkage maps for tiger grouper (Epinephelus fuscoguttatus) and giant grouper (E. lanceolatus) using 399 simple sequence repeat markers and performed a quantitative trait locus (QTL) analysis to identify the genomic regions responsible for growth‐related traits in F1 hybrid grouper (E. fuscoguttatus × E. lanceolatus). The tiger grouper (female) linkage map contained 330 markers assigned to 24 linkage groups (LGs) and spanned 1,202.0 cM. The giant grouper (male) linkage map contained 231 markers distributed in 24 LGs and spanned 953.7 cM. Six QTLs affecting growth‐related traits with 5% genome‐wide significance were detected on different LGs. Four QTLs were identified for total length and body weight on Efu_LG8, 10, 13 and 19 on the tiger grouper map, which explained 6.6%–12.0% of the phenotypic variance. An epistatic QTL with a reciprocal association was observed between Efu_LG8 and 10. Two QTLs were identified for body weight on Ela_LG3 and 10 on the giant grouper map, which explained 6.9% of the phenotypic variance. Two‐way analysis of variance indicated that the QTL on Efu_LG13 interacts with the QTLs on Ela_LG3 and 10 with large effects on body weight. Furthermore, these six QTLs showed different features among the winter, summer and rainy seasons, suggesting that environmental factors and fish age affected these QTLs. These findings will be useful to understand the genetic structure of growth and conduct genetic breeding in grouper species.

A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication

“…Studies on other teleost species, including stickleback, have also reported detailed empirical evidence of sexually dimorphic recombination rates, calculating female:male recombination ratios of linkage map lengths to be 1.64 (Sardell et al 2018). Future work should aim to compare and contrast the recombination landscape of whitefish to the detailed sexually dimorphic recombination patterns observed in drosophila, mice, deer and various fish species (Dunn 1920; Sakamoto et al 2000; Lenormand and Dutheil 2005; Johnston et al 2017; Kubota et al 2017; Sardell et al 2018).…”

“…Linkage maps have become an essential tool in investigating evolution in non-model systems, providing information about the relative locations of markers along the genome and assisting in the assembly of new de novo genomes (Ellegren 2013; da Fonseca et al 2016; Sutherland et al 2016; Kubota et al 2017; Sun et al 2017; Zhigunov et al 2017; Matz 2018). Many non-model organisms have specific ecological and evolutionary characteristics which make them particularly interesting for asking targeted evolutionary questions (Matz 2018).…”