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 6,360.12 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.

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

“…Ross D Houston, C. Kriaridou and D. Robledo Animal 16 (2022) 100642 Juárez et al, 2007;Lu et al, 2016Lu et al, , 2017Trang et al, 2019;Giang et al, 2019;Luan et al, 2020;Lillehammer et al, 2020) QTL analysis (5) (Yu et al, 2015;Huang et al 2020a;2020b;Peng et al, 2020;Zeng et al, 2020 (Rutten et al, 2005a;2005b;Charo-Karisa et al, 2005, 2006Lozano et al, 2013;Yoshida et al, 2017;Shoemaker et al, 2017;De Verdal et al, 2018;Workagegn et al, 2020;Mengistu et al, 2020Mengistu et al, , 2021Barría et al, 2021a,b;da Cardoso et al, 2021 QTL analysis (12) (Eshel et al, 2011(Eshel et al, , 2012Lühmann et al, 2012;Palaiokostas et al, 2013Palaiokostas et al, , 2015Liu et al, 2014;Gu et al, 2018;Jiang et al, 2019;Cáceres et al, Mass selection for growth (Liang et al, 2019) Genetic parameters (5) (Zhao et al, 2012;Yan et al, 2014;Huo et al, 2017;…”

Bulk segregation analysis in the NGS era: a review of its teenage years

“…In addition, the traits required for BSA mapping have gradually shifted from qualitative traits to quantitative traits controlled by major genes (such as disease resistance traits) (Aoun et al., 2017; Hyten et al., 2009; Shoba et al., 2012). Some researchers have also attempted to use BSA mapping for complex quantitative traits (Salunkhe et al., 2011; Sun et al., 2010; Zeng et al., 2020).…”