A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance

Abstract

Simple sequence repeats (SSRs) of short nucleotide motifs occur very frequently in the 5′ untranslated coding region (5′-UTR) of genes and have been implicated in the regulation of gene expression. In this study, we identified an SSR with a variable number of CT repeats in the 5′-UTR of the Litopenaeus vannamei IRF (LvIRF) gene that has been shown to mediate antiviral responses by inducing the expression of Vago, a functional homolog of mammalian IFN. We then explored the effects of varying the number of (CT)n repeats on the expression of LvIRF using both dual-luciferase reporter assays and Western blots. Our results demonstrate that the length of the (CT)n-SSR in this gene can influence the expressional level of LvIRF, in that a shorter (CT)n repeat had a stronger ability to induce the expression of LvIRF. Moreover, we found that the (CT)n repeat in LvIRF was associated with viral resistance in shrimp. Individual shrimps with shorter (CT)n repeats in the 5′-UTR of LvIRF exhibited high tolerance to white spot syndrome virus (WSSV), and this trait was inherited in offspring. Taken together, these results indicated that this (CT)n-SSR could be used as a molecular marker for shrimp breeding for WSSV resistance.

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp

“…Further studies of SSRs will help us understand the penaeid shrimp genomes better and extend its utilization in many more scientific areas. For example, SSR length polymorphisms have been shown to play important roles in viral resistance in various aquaculture populations of L. vannamei 47 . As the most important economic shrimp group all over the world, penaeids are widely cultured, and future utilization of the potential functions of SSRs will promote the selective breeding of these organisms.…”

Recent advances in crustacean genomics and their potential application in aquaculture

“… 56,61–64 Therefore, high SSR content is one of the most unique genomic characteristics of crustaceans compared to other animals. The proliferation of SSRs has been suggested to drive remarkable genome plasticity and regulate gene expression for adaptive evolution 61,62,65 . In addition, SSRs can influence gene activity in shrimp, including virus resistance, suggesting their potential applications in aquaculture 65 .…”

“…The proliferation of SSRs has been suggested to drive remarkable genome plasticity and regulate gene expression for adaptive evolution 61,62,65 . In addition, SSRs can influence gene activity in shrimp, including virus resistance, suggesting their potential applications in aquaculture 65 . Moreover, SSR markers are enormously useful in the characterization of population structure, genetic mapping and evolutionary processes 66 …”

Design of microsatellite markers for Schizophyllum commune (Agaricales, Basidiomycota) based on analysis of its genome

“…Протягом останніх років SSR є найпопулярнішим джерелом генетичних маркерів та широко використовуються у типізації штамів, популяційній генетиці, філогенетиці та генетичному картуванні (Kirungu et al, 2018;Wang et al, 2017;Liu et al, 2020). Крім того, останні дослідження показують, що мікросателіти виконують функціональну роль, впливаючи на регуляцію роботи генів, транскрипцію, функцію синтеза білка та організацію геному в цілому (Gerber et al, 1994;Hefferon et al, 2004;Kashi, King, 2006;Singh et al, 2018;Yin et al, 2019). Відомо, що варіації мікросателітів в основному спричинені неправильним з'єднанням послідовностей ДНК та подальшим збереженням помилок під час реплікації, репарації та рекомбінації (Schllotteroer et al, 1991).…”