Construction of a genetic linkage map, QTLs mapping for low salinity and growth-related traits and identification of the candidate genes in Pacific white shrimp (Litopenaeus vannamei)

Abstract

Low-salinity tolerance and growth are crucial economic traits of shrimp in areas with low-salinity water. In the current study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was obtained by the “semidirectional cross” method, and 2 parents and 146 progenies were genotyped using double-digest restriction site-associated DNA sequencing technology (ddRAD-Seq). A total of 3335 high-quality markers were identified and used to construct a genetic linkage map. This genetic map comprised 48 linkage groups (LGs), and the total map length spanned 3954.462 centimorgan (cM) with an average marker interval of 1.186 cM. Three quantitative trait loci (QTLs) for low-salinity tolerance and 3 QTLs for growth (body weight) were detected under the condition of restricted logarithmic odds (LOD) score ≥ 2.50. With the assistance of the genome of L. vannamei and relevant annotations, 3 potential growth-related genes (sob, TJP1 and ZBTB24) and 3 low-salinity response candidate genes (Rnf168, CNOT2 and RPB3) were identified from the genomic scaffolds. Moreover, the qPCR results showed that the expression levels of the 3 candidate genes were significantly affected by low-salinity stress, indicating that they possibly play an important role in low-salinity stress. Here, we present the first report of mapping of low-salinity tolerance QTLs in the genetic mapping of L. vannamei, which will be beneficial for the selection of shrimp breeding markers and might help promote the study of the L. vannamei genome.