A simple sequence repeats marker of disease resistance in shrimp Litopenaeus vannamei and its application in selective breeding

Abstract

The polymorphism of the simple sequence repeat (SSR) in the 5' untranslated coding region (5'-UTR) of the antiviral gene IRF (LvIRF) has been shown to be implicated in the resistance to viral pathogens in shrimp Litopenaeus vannamei (L. vannamei). In this study, we explored the potential of this (CT)n-SSR marker in disease resistance breeding and the hereditary property of disease resistance traits in offspring. From 2018 to 2021, eight populations were generated through crossbreeding by selecting individuals according to microsatellite genotyping. Our results demonstrated that shrimp with the shorter (CT)n repeat exhibited higher resistance to white spot syndrome virus (WSSV) or Decapod iridescent virus 1 (DIV1); meanwhile, these resistance traits could be inherited in offspring. Interestingly, we observed that the longer (CT)n repeats were associated with bacterial resistance traits. Accordingly, shrimp with longer (CT)n repeats exhibited higher tolerance to Vibrio parahaemolyticus infection. Taken together, these results indicate that the single (CT)n-SSR marker could be used to selective breeding for both resistance to virus and bacteria in shrimps.

Keywords: IRF; disease resistance; selective breeding; shrimp; simple sequence repeat (SSR).

FIGURE 1

Schematic representation of the selective population. The HX150301 and HX1403 populations as founder stocks, with LvIRF-SSR genotyping used to select individuals as parents for cross-matching to obtain F1 in 2019. Based on F1, the same method was used for breeding F2 and F3 in 2020 and 2021, respectively. The homozygous populations CTSS and CTSS02, as well as the heterozygous populations CTS02 and CTS03, were separated from CTS with LvIRF-SSR genotyping.

FIGURE 2

Genotyped of LvIRF-SSR in F2 and F3. (A–C) The allelic distribution in F2 three populations: CTSS (A), CTS02 (B) and CTL02 (C). (D–F) The allelic distribution in F3 three populations: CTSS02 (D), CTS03 (E) and CTL03 (F).

FIGURE 3

Differences in antiviral traits between shrimp populations in F2 and F3. (A,C) Cumulative mortality of F2 populations infected with WSSV and DIV1. (B,D) The expression of LvIRF in the gill after WSSV and DIV1 infection. (E,G) Cumulative mortality of F3 populations infected with WSSV and DIV1. (F,H) The expression of LvIRF in the gill after WSSV and DIV1 infection. Cumulative mortality data were analyzed statistically by the Kaplan ± Meier plot (log-rank χ² test). *p < 0.05, **p < 0.01, ***p < 0.001, ns, not significant. Quantitative RT-PCR was performed for each sample using the LvEF-1α gene as an internal control by the Livak (2^−ΔΔCT) method. Expression levels in the gill were used to determine the mean fold change (means ± SD, n = 9. *p < 0.05, **p < 0.01, ***p < 0.001, ns, not significant.

FIGURE 4

Differences in Vibrio parahaemolyticus resistance between shrimp populations in F2 and F3. (A) Analysis of Vibrio parahaemolyticus resistance differences among the three populations in F2. (B) Analysis of VP resistance differences among the three populations in F2. Cumulative mortality data were analyzed statistically by the Kaplan ± Meier plot (log-rank χ² test). **p < 0.01, ***p < 0.001, ns, not significant.

FIGURE 5

Differences in growth traits between shrimp populations in F2. (A) Analysis of body length differences among the three populations in F2. (B) Analysis of body weight differences among the three populations in F2. ***p < 0.001, ns, not significant.