Molecular markers and their application in genetic diversity of penaeid shrimp

Penaeidae is a family of shrimp, and it contains many species of economic importance, such as the tiger prawn (Penaeus monodon), white leg shrimp, Atlantic white shrimp and Indian prawn. Identification and population genotype structure of penaeid shrimp have been enhanced by molecular markers that can be classified into three types, namely allozyme, mitochondrial and nuclear markers. The widely used mitochondrial DNA markers are 12S rDNA, 16S rDNA, cytochrome b and control region. Random amplification of polymorphic DNA, amplified fragment length polymorphism, restriction fragment length polymorphism, single-stranded conformational polymorphism and microsatellites are the most commonly used nuclear markers for DNA fingerprinting. Molecular markers play a crucial role in penaeid shrimp to evaluate phenotypic and genetic variation, assess demographic bottleneck, study natural population structure, compare wild and hatchery populations, preserve genetic biodiversity, construct chromosome maps and detect whether genetic tag propagation–assisted rehabilitation programs are effective. Increase in the number of molecular markers, construction of high-density genetic maps and implementation of genomic resources (including genome sequencing) are expected to provide tools for the genetic improvement in these aquaculture species through marker-assisted selection. Molecular markers are versatile tools for the identification of populations with genetic crisis by comparing genetic diversities, which helps to establish management units within these threatened species.