Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

Abstract

Background Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. Results In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41–8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance. Conclusions In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding.

Genome-wide association study identified genes associated with ammonia nitrogen tolerance in Litopenaeus vannamei

“…A number of SNPs significantly associated with ammonia nitrogen tolerance were identified by using MLM, FarmCPU and Blink models. However, the p -value of these SNPs is relatively low, which could confirm previous speculations that ammonia nitrogen tolerance is highly polygenic and may be controlled by many genes with moderate to low effects ( Lu et al, 2016 ; Zeng et al, 2020 ).…”

“…Quantitative trait loci (QTL) linkage mapping is an essential method for identifying relevant genes. Zeng et al (2020) constructed a high-density genetic map of L. vannamei and mapped a QTL associated with ammonia nitrogen tolerance. Due to limitations of marker density, QTL analysis only identified one gene, LOC113809108, annotated as the ATP synthase g subunit.…”

“…Quantitative trait loci (QTL) linkage mapping is an essential method for identifying relevant genes. Zeng et al (2020) constructed a high-density genetic map of L . vannamei and mapped a QTL associated with ammonia nitrogen tolerance.…”

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)

“…U. unicinctus , L. vannamei , and C. teleta are three typical pollutant-tolerant benthos that live in the intertidal zone. Among them, L. vannamei was reported to be resistant to a variety of pollutants, including nitrite [ 43 ], ammonia [ 44 ], sulfide [ 21 ], etc. C. teleta is a sediment-dwelling marine polychaete that is described as a pollution indicator species and is often found in disturbed or stressed organically and sulfide-enriched environments [ 45 , 46 ].…”

A Review of the Emerging Risks of Acute Ammonia Nitrogen Toxicity to Aquatic Decapod Crustaceans

“…Ammonia nitrogen is commonly considered the primary factor that can rapidly cause increased shrimp mortality. It was reported that the 96 h LC 50 of TAN in the adult black tiger shrimp Penaeus monodon was 65 mg/L [35], and the 72 h LC 50 of TAN in the adult Pacific shrimp was 345.94 mg/L [36]. Furthermore, our previous study demonstrated that the red swamp crayfish Procambarus clarkii with a larger size exhibited a higher and stronger antioxidant capacity, thus exerting a higher tolerance to ammonia stress [37].…”