Correlation between SNPs in promoter region of gene, L-Type lectin (LvLTLC1) and the resistance trait of shrimp, Litopenaeus vannamei, against vibrios

Pacific white shrimp, Litopenaeus vannamei ( L. vannamei ), is the most economically valuable shrimp species in world. Bacterial diseases mainly caused by various vibrios bring huge economic loss in shrimp aquaculture. Previous research has confirmed that LvLTLC1 gene coding a L-type lectin of L. vannamei plays a pivotal role in the resistance of shrimp against pathogenic vibrios, which implies the potential of LvLTLC1 as a target gene to develop SNP markers for genetic breeding of the shrimp. In this study, pan-vibrio resistance (PVR) trait of L. vannamei was quantitatively evaluated by vibrios loads in hepatopancreas and shrimp individuals were divided into vibrios-resistance (VR) groups and vibrios-susceptible (VS) groups according to their vibrios-resistance performance (VRP). Expression assay of LvLTLC1 showed that mRNA levels of LvLTLC1 in the hepatopancreas of the VR group was significantly higher than that in the VS groups. Totally, 24 SNPs were identified in the promoter regions of LvLTLC1 in shrimp individuals. Correlation analysis between the genotypes of these single nucleotide polymorphism (SNPs) and the VRP revealed that a homozygous GG genotype in SNP8 (g.–256 A/G) were significantly correlated with the VRP ( P < 0.05). Linkage disequilibrium (LD) analysis revealed a high linkage block of SNP9 (g.–249 T/G) and SNP10 (g.–235 A/G), and a TT/GG combined genotype of SNP9 and SNP10 was further discovered to be significantly associated with strong VRP ( P < 0.05). Furthermore, the variations in motifs caused by SNP8, SNP9, and SNP10 led to changes of binding patterns of transcription factors. The present study first revealed the presence of abundant SNPs in a gene promoter region of shrimp L. vannamei and found that specific genotypes of SNPs in LvLTLC1 promoter confer strong VRP in the shrimp. The homozygous GG genotype in SNP8 and the TT/GG genotype combination of SNP9 and SNP10 can be served as two potential molecular markers for the PVR trait in genetic breeding of L. vannamei. • First put forward a concept of pan-vibrios resistance trait in shrimp. • Developing a method to grade pan-vibrios resistance trait of L. vannamei . • Genetic variations were initially revealed in the gene promoter of L. vannamei . • A SNP molecular marker associated with pan-vibrios resistance trait was successfully developed.