Construction of a high-density genetic linkage map and QTL mapping for sex and growth traits in Artemia franciscana

Abstract Artemia is not only one of the most important live feed used in larviculture, but also an ideal experimental organism for scientific research. In the study, SLAF-seq method was used to develop SNP markers and construct the first high-density genetic linkage map for Artemia franciscana. A total of 8709 effective SNP markers were mapped into 21 linkage groups by using one full-sib family with 106 progenies. The map spanned 2636.43 cM and 105 loci per LG, with an average inter-marker distance of 1.19 cM. QTL mapping analysis revealed that one major sex-related QTL containing 466 sex-related SNP markers on LG6, with the most significant locus explained 100% of the phenotype variance. Given of the presence of 15 female-specific SNPs, their segregation patterns and the lower female/male recombination, the WZ-ZZ sex determining system was further confirmed in A. franciscana. Meanwhile, seven QTLs associated with growth-related traits were found within three intervals on LG6, highlighting the possible involvement of LG6 in both growth and phenotypic sex. QTL-association analysis further identified 22 candidate genes that probably related to the biological process of reproduction, growth and immunity. Our results provide a valuable resource for genetic improvement and genome study of Artemia.