High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species. In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8–15.7% of the total growth-traits variation. The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

Saline–alkaline water limits the growth and survival of aquatic animals due to its high carbonate alkalinity, high pH, and various ion imbalances. The ridgetail white prawn Exopalaemon carinicauda is strongly adaptable to the saline–alkaline water, making it an excellent candidate species for large-scale aquaculture in saline–alkaline areas. To explore the effect of long-term high carbonate alkalinity stress on ovarian development in E. carinicauda for assisting the development of saline–alkaline aquaculture, we performed ovary histology analysis and RNA–sequencing of the eyestalk and ovary in order to compare the transcriptomic responses of individuals in high carbonate alkalinity (8 mmol/L) with a control group (2 mmol/L) for 60 days. It was found that high carbonate alkalinity stress resulted in a loose arrangement of oogonia and a small number of surrounding follicular cells. A total of 1102 differentially expressed genes (DEGs) in ovary tissue were identified under high carbonate alkalinity stress, and the 18 important DEGs were associated with ovarian development. The majority of the DEGs were enriched in ECM–receptor interaction, Folate biosynthesis, the FoxO signaling pathway, insect hormone biosynthesis, and lysosome, which were involved in the ovarian development of E. carinicauda. A total of 468 DEGs were identified in eyestalk tissue under high carbonate alkalinity stress, and the 13 important DEGs were associated with ovarian development. KEGG enrichment analysis found that ECM–receptor interaction, folate biosynthesis, lysosome, metabolic pathways, and retinol metabolism may be involved in the ovarian development under high carbonate alkalinity stress. Our results provide new insights and reveal the genes and pathways involved in the ovarian development of E. carinicauda under long-term high carbonate alkalinity stress.

The Exopalaemon carinicauda could be a useful crustacean laboratory animal in many research fields. We newly established an inbred line of Exopalaemon carinicauda named EC4 inbred line by brother×sister mating and keeping to F₁₁ generation. Trends in heterozygosity in the process of producing EC4 inbred line were examined through the characterization of polymorphisms based on gene frequencies of SNP and EST-SSR loci. The results demonstrated that the number of alleles (N), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) gradually decreased with the increase of inbreeding generations. The genetic detection results indicated that 9 (29.03%, 9/31) of the SNP loci and 15 (32.61%, 15/46) of the EST-SSR loci were homozygous in F₁₁ generation of EC4 inbred line. The variation of the growth-related traits, the immune responses, and antioxidant status were described in experimental full-sibling inbred populations of E. carinicauda at five levels of inbreeding coefficient (F=0.785, F=0.816, F=0.859, F=0.886, F=0.908) under controlled laboratory conditions. The body weight, body length, and survival rate in EC4 inbred line of all generations were less than the control population. Inbreeding affected the antibacterial activity, phenoloxidase (PO) activity, and superoxide dismutase (SOD) which decreased at the eleventh generation of EC4 inbred line. This study demonstrated that inbreeding had a negative effect on the economic traits and immune response, but our inbred line was established successfully until F₁₁ and confirmed by genetic detection using SNP and EST-SSR loci.