Identification and characterisation of microsatellite DNA markers in order to recognise the WSSV susceptible populations of marine giant black tiger shrimp, Penaeus monodon

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

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.

Identification and characterization of novel microRNAs in disease-resistant and disease-susceptible Penaeus monodon

MicroRNAs (miRNAs), known as a translational regulator, are evolutionary conserved, small, and noncoding RNA. They have played a vital role in disease biology through the host-virus-miRNA-interaction. In this study, novel miRNAs of naturally occurring, virus-free disease-resistant and disease-susceptible Penaeus monodon were identified and characterized. In disease-susceptible samples, 45 homologous mature miRNAs and 28 homologous precursor miRNAs were identified. In disease-resistant samples, 52 homologous mature miRNAs and 87 homologous precursor miRNAs were identified. In disease-susceptible samples, 33 novel mature miRNAs and 33 novel precursor miRNAs were identified. In disease-resistant samples, 523 novel mature miRNAs and 141 novel precursor miRNAs were identified. Differential expression study revealed the up-regulated and down-regulated miRNAs in disease-resistant and disease-susceptible P. monodon. Gene ontology pathway of known and novel miRNAs revealed that P. monodon miRNAs might have a potential and specific role in signal transduction, cell-to-cell signaling, innate immune response and defense response to different pathogens.

Development and characterization of white spot disease linked microsatellite DNA markers in Penaeus monodon, and their application to determine the population diversity, cluster and structure

Pathogens that are introduced suddenly to natural populations can potentially cause quick changes to the genetics and diversity of the host. In the past three decades, white spot syndrome virus (WSSV) has caused damaging epizootics in Penaeus monodon populations. In this study, we developed WSSV resistance- or susceptibility-linked microsatellite DNA markers, and their effectiveness was validated experimentally. WSSV-resistant marker linked retroelements and genes that may have an important role in WSSV-resistance phenomena were partially identified. Allelic data of 1,694 samples from nine distinct geographic locations in India were revealed that populations from Digha and Kochi were highly dispersed, and also showed higher genetic diversity, higher population diversity, and lower prevalence of disease resistance. A very high level of gene flow was observed within all populations and a very high level of genetic variation was present within populations. Two genetically admixture population clusters were estimated in nature. WSSV-resistance has a significant link with genetic diversity, population cluster and population diversity. Microsatellite marker analysis characterized genetic divergence, diversity and structure among wild populations.