Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci for Nitrite Tolerance in the Pacific White Shrimp (Litopenaeus vannamei)

Abstract

Nitrite is a major environmental toxin in aquaculture systems that disrupts multiple physiological functions in aquatic animals. Although nitrite tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. In this study, we constructed a high-density genetic map of Litopenaeus vannamei with 17,242 single nucleotide polymorphism markers spanning 6,828.06 centimorgans (cM), with an average distance of 0.4 cM between adjacent markers on 44 linkage groups (LGs). Using this genetic map, we identified two markers associated with nitrite tolerance. We then sequenced the transcriptomes of the most nitrite-tolerant and nitritesensitive individuals from each of four genetically distinct L. vannamei families (LV-I-4). We found 2,002, 1,983, 1,954, and 1,867 differentially expressed genes in families LV-1, LV-2, LV-3, and LV-4, respectively. By integrating QTL and transcriptomics analyses, we identified a candidate gene associated with nitrite tolerance. This gene was annotated as solute carrier family 26 member 6 (SLC26A6). RNA interference (RNAi) analysis demonstrated that SLC26A6 was critical for nitrite tolerance in L. vannamei. The present study increases our understanding of the molecular mechanisms underlying nitrite tolerance in shrimp and provides a basis for molecular-marker-assisted shrimp breeding.

Shrimp immune response: A transcriptomic perspective

“…As example of the appli- Molecular markers based on single nucleotide polymorphisms (SNPs) have been recently implemented for selecting for growth performance, 113,114 resistance to V. parahaemolyticus in P. vannamei, 111,115 parvovirus in P. mergulensis 116 or even different stressors such as nitrite concentration. 117 Recently, Pooljun et al 118 have found an association between a SNP in the anti-lipopolysaccharide factor 3 (ALF3) and resistance to WSSV in P. monodon. These results open a new way to fight against the different diseases that threaten the industry with massive pathogenic outbreaks.…”

Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

“…High-density genetic maps are essential and helpful for genome assembly at higher levels, comparative genomic analysis, and fine mapping of complex traits. To date, with the rapid development and application of high-throughput sequencing technology, high-density genetic maps of aquatic shrimps, including Litopenaeus vannamei ( Peng et al, 2020 ; Yu et al, 2015 ; Zhang et al, 2007 ), Penaeus monodon ( Guo et al, 2019 ; Wilson et al, 2002 ), and Fenneropenaeus chinensis ( Li et al, 2006 ; Wang et al, 2012 ), have been completed for reduced-representation genome sequencing. Based on this, the genetic mechanisms underlying sex determination have also been explored.…”