1.1 Introduction
Shrimp farming is an important animal production activity with over 40 years of existence (Chamberlain, 2010; FAO, 2018). Its importance relies on its great ability to expand to developing countries, contributing to improve their economy, providing an income to vulnerable populations and producing high-quality animal protein for human consumption (Pillay & Kutty, 2005; Escobedo-Bonilla, 2013). In 2016, farmed shrimp production reached 4.9 million tonnes, the most farmed species being Litopenaeus vannamei (86%) and Penaeus monodon (14%), respectively (FAO, 2018).
Since its beginning, shrimp aquaculture has sought to improve not just the culture techniques but also the shrimp species used in the industry in order to increase production. Appealing traits of farmed shrimp include ease of breeding and high spawning rate, fast growth and size, its ability to acclimate to changing environment factors, efficient feed conversion rate and pathogen resistance (Briggs et al., 2005; Pillay & Kutty, 2005; Leu et al., 2011; Yuan et al., 2018).
Programs aimed to produce domesticated shrimp arose in the 1970sâ1980s in Tahiti and the USA, which produced shrimp lines of specific pathogen-free and specific pathogen-resistant strains of shrimp for farming purposes (Briggs et al., 2005; Wyban, 2007; Lightner, 2011). Although these programs focused on phenotypic traits such as growth rate and pathogen-free or pathogen-resistant status, such shrimp still showed performance pitfalls depending on various environmental and/or management factors (Schuur, 2003; Briggs et al., 2005; Moss et al., 2012). These were the first attempts to manipulate shrimp population genomics through phenotypic features.
With the development of molecular tools, it is possible to study the relationship between certain desired features and the genes involved with them. Various techniques have been developed in the last two decades to obtain transcriptomic information, including expressed sequence tags (EST), cDNA microarrays, suppression subtractive hybridization (SSH) and next-generation sequencing (NGS) (Robalino et al., 2007; Leelatanawit et al., 2008; Leu et al., 2011; Li et al., 2012). These tools have increased the knowledge on gene expression and the function of various aspects of shrimp life cycles, genome organization, gene function, physiology of key processes such as reproduction, sex determination, development and growth, digestion, defense function and tolerance to environmental stress. Transcriptomics will help to improve the way to regulate sex ratios in farmed and wild animal populations, expanding growth rates in shorter times and increasing disease resistance, among other traits (Santos et al., 2014; Chandhini & Rejish-Kumar, 2019).
1.2 Transcriptomic Methods
1.2.1 Expressed Sequence Tags (ESTs)
The first technique used to generate transcriptomic data from organisms with unknown genomes was the expressed sequence tags (ESTs). Here, randomly sequenced cDNA clones from a cDNA library produced short sequences (Leu et al., 2011). Further, ESTs were used to describe transcribed regions of a genome in tissues under specific conditions. This method has been an important source for gene identification and structure, novel alleles, characterization of single nucleotide polymorphism (SNP) and genome annotation (OâLeary et al., 2006; Leu et al., 2011).
The random cDNA sequencing has generated from 190 up to a maximum of 13,700 ESTs with a size ranging from 200 to 800 base pairs (bp) (Cesar et al., 2008; Leu et al., 2011). The use of ESTs has been done on various shrimp species, most of which are used in aquaculture: Litopenaeus vannamei, L. setiferus (Gross et al., 2001; OâLeary et al., 2006), Penaeus monodon (Tassanakajon et al., 2006; Leelatanawit et al., 2008), Marsupenaeus japonicus (Yamano & Unuma, 2006) and Fenneropenaeus chinensis (Xiang et al., 2008).
Studies using ESTs have produced putative gene sequences ranging from 44 to nearly 7,500 reported with this method (Table 1.1). These gene sequences are related to the following known or potential functions: defense, putative receptor, signal transduction or hormonal function, sex differentiation and reproduction, growth, cell shape, motility, extracellular matrix, DNA replication and repair, transcription/translation and ribosomal RNAs, metabolism and homeostasis, digestive functions, transport, membrane structure and channel proteins, lysosomal and proteosomal genes (Table 1.2). Other ESTs produced gene sequences different from those listed previously as well as genes of unknown function and novel sequences with no matches in public databases (Gross et al., 2001; Tassanakajon et al., 2006; Leu et al., 2011). In P. monodon postlarvae, analyses showed a total of 6,671 EST related to 624 genes of which...
