**5. Marker‐assisted selection of growth and disease resistance traits**

#### **5.1. Growth traits**

Genetic selection in which individuals with the best growth traits are selected as parent stock for the next generation is one of the major strategies used for improving production in aqua‐ culture. And as such, several breeding programmes have been going on using natural selec‐ tion approaches [141–143]. The major drawback with this approach is that it takes several generation cycles to identify individuals having positive growth traits. To expedite the pro‐ cess of identifying genetic traits for optimal growth performance, marker‐assisted selection (MAS) processes such as single nucleotides polymorphism (SNP), microsatellite, amplified fragment length polymorphism (AFLP), random amplified polymorphism DNA (RAPD), restriction fragment length polymorphism (RFLP) and quantitative trait loci (QTL) are being used to scan chromosomal DNA of different farmed aquatic organisms. Among these, the most widely used is QTL analysis, which has been applied across most of the commercial fish and crustacean species used in aquaculture [144–147]. As defined by Geldermann [148], QTLs are chromosomal regions made of single genes or gene clusters determining a quantitative character of a given trait. Given their high heritability, mapped QTLs have proved to be a useful tool in selective breeding, which has played an important role in accelerating genetic improvement in aquaculture.

As shown in **Tables 1** and **2**, the most important genetic traits sought for in aquaculture are growth rate, body weight and length. These traits influence the commercial value of farmed aquatic organisms. Traits for body weight and length have been identified in several fish spe‐ cies such as Atlantic salmon [149], rainbow trout [150], Big heard carp (*H. nobilis*) [151], common carp [152, 153] and tilapia (*Oreochromis niloticus*) [154], nine spined stickleback (*Pungitius pun‐ gitius*) [155] and Arctic char (*Salvelinus alpinus*) [156]. In shrimps and prawns, body weight and length traits have been identified in kruma shrimp [157, 158], Chinese shrimp [159], Giant fresh water prawn [160], Ridge white prawn [161] and Oriental river prawns [162]. Another impor‐ tant trait, which has contributed to improved production in aquaculture is sexual maturation. It has been shown that in some some species, sex is closely related to growth. For example, Sun and Liang [163] showed that in common carp, females grow bigger than males at the same age, while in tilapia, the males grow faster than females [164]. Hence, the selection of males for aquaculture increases production in tilapia while the females increase production in carp. Important traits related to improving meat quality include muscle quality [154], muscle fibre [165], texture [165], colour [166, 167], fat percentage [166] and dressed weight percentage [166].


**Table 1.** Growth and performance traits for different fish species.

antigen designated as Esa1, which they used to produce a DNA vaccine against *E. tarda* in Japanese flounder. They showed that the pCEsa1 vaccine enhanced respiratory burst, acid phosphatase activity and bactericidal activity of headkidney macrophages. In addition, it produced RPS = 57% in passively vaccinated fish. Overall, these studies show that genomics approaches can be used to identify the most immunogenic proteins for different bacterial

strains in order to produce the most protective vaccines for use in aquaculture.

182 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

**5.1. Growth traits**

improvement in aquaculture.

**5. Marker‐assisted selection of growth and disease resistance traits**

Genetic selection in which individuals with the best growth traits are selected as parent stock for the next generation is one of the major strategies used for improving production in aqua‐ culture. And as such, several breeding programmes have been going on using natural selec‐ tion approaches [141–143]. The major drawback with this approach is that it takes several generation cycles to identify individuals having positive growth traits. To expedite the pro‐ cess of identifying genetic traits for optimal growth performance, marker‐assisted selection (MAS) processes such as single nucleotides polymorphism (SNP), microsatellite, amplified fragment length polymorphism (AFLP), random amplified polymorphism DNA (RAPD), restriction fragment length polymorphism (RFLP) and quantitative trait loci (QTL) are being used to scan chromosomal DNA of different farmed aquatic organisms. Among these, the most widely used is QTL analysis, which has been applied across most of the commercial fish and crustacean species used in aquaculture [144–147]. As defined by Geldermann [148], QTLs are chromosomal regions made of single genes or gene clusters determining a quantitative character of a given trait. Given their high heritability, mapped QTLs have proved to be a useful tool in selective breeding, which has played an important role in accelerating genetic

As shown in **Tables 1** and **2**, the most important genetic traits sought for in aquaculture are growth rate, body weight and length. These traits influence the commercial value of farmed aquatic organisms. Traits for body weight and length have been identified in several fish spe‐ cies such as Atlantic salmon [149], rainbow trout [150], Big heard carp (*H. nobilis*) [151], common carp [152, 153] and tilapia (*Oreochromis niloticus*) [154], nine spined stickleback (*Pungitius pun‐ gitius*) [155] and Arctic char (*Salvelinus alpinus*) [156]. In shrimps and prawns, body weight and length traits have been identified in kruma shrimp [157, 158], Chinese shrimp [159], Giant fresh water prawn [160], Ridge white prawn [161] and Oriental river prawns [162]. Another impor‐ tant trait, which has contributed to improved production in aquaculture is sexual maturation. It has been shown that in some some species, sex is closely related to growth. For example, Sun and Liang [163] showed that in common carp, females grow bigger than males at the same age, while in tilapia, the males grow faster than females [164]. Hence, the selection of males for aquaculture increases production in tilapia while the females increase production in carp. Important traits related to improving meat quality include muscle quality [154], muscle fibre [165], texture [165], colour [166, 167], fat percentage [166] and dressed weight percentage [166].


burden and prevent the use of antibiotics, which have been shown to have adverse environ‐ mental effects, there has been a tremendous increase in genomics studies aimed at identify‐ ing disease resistance traits in different cultured organisms. And as such, different approaches such as SNP, MTLS, AFLP, RAPD, RFLP and QTL analyses have been used for the iden‐ tification of disease resistance and susceptibility traits in different aquatic organisms. In the case of fish viral diseases, QTL resistance traits have been generated for grass cap reo‐ virus (GCRV) infection in grass carp [179], nervous necrosis virus (NNV) in seabass [180], viral hemorrhagic septicemia (VHS) in turbot [181] and rainbow trout [182], infectious salmon anaemia (ISAV) virus in Atlantic salmon, lymphocytic disease virus in Japanese flounder [183] and infectious pancreatic necrosis virus (IPNV) in Atlantic salmon [184, 185]. Among these, the QTL for resistance against IPNV has contributed to significantly reducing the IPNV incidence by >80% from 2008 when IPNV resistance fish were introduced in the Norwegian Atlantic salmon indus‐ try to 2015 [186]. Bacteria disease for which QTL resistance traits have been identified include coldwater disease in rainbow trout [187], *Aeromonas hydrophila* in rohu (*Labeo rohita*) [188], *Vibrio anguillarum* in Japanese flounder [189], *Flavobacterium psychrophilum* in rainbow trout [190] and pastuerellosis in Gilhead seabream [191]. As for parasitic diseases, QTL resistance traits have been identified for *Gyrodactylus salaris* in Atlantic salmon [192] and Monohenean parasite (*Benedenia* 

Current Advances in Functional Genomics in Aquaculture

http://dx.doi.org/10.5772/intechopen.69883

185

In shrimps, resistance traits have been identified for white spot syndrome virus (WSSV) in Indian black tiger shrimp (*Penaeus monodon*) [194, 195], Fenneropenaeus (*Penaeus chinensis*), infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance in shrimp (*Litopenaeus stylirostris*) [196] and taura syndrome resistance in Pacific white shrimp (*P. van‐ namei*) [197]. Among these, the QTL for resistance against TSV has contributed to significant reduction of the disease prevalence in shrimps by generating pathogen‐specific free disease

The term 'epigenetics' was first coined by Waddington in 1942 and was defined as changes in the phenotype without inducing changes in the genotype [198, 199]. Studies on chemical modifica‐ tion of DNA bases date as far back as 1948 [200] and by the 1970s, the role of DNA methylation in gene regulation was identified [201]. In subsequent years, the link between DNA methylation and gene expression was established [202] paving way to the discovery of therapeutic drugs such as 5‐azacytidine used to block DNA methylation [203]. In principle, epigenetic changes are regulated by (i) chemical modifications on DNA cytosine residues resulting in DNA methylation and, (ii) histone protein modifications on DNA [204, 205]. Current advances in HTS have refined genomic analyses to base‐pair resolution making it easier to map entire epigenomes of living organ‐ isms enabling us to identify biological markers predictive of the outcome of disease infections, reproduction, growth and adaptation to new environments [206]. As a result of these advances, epigenetics studies in aquaculture have tremendously increased in the last decades with the view to identifying biological markers relevant for improving the production of farmed aquatic organisms. Technologies used for epigenetics analyses in aquaculture include (i) RNA‐seq in

*seriolae*) in Yellow tail (*Seriola quinqueradiata*) [193].

shrimps for us in breeding programmes in aquaculture.

**6. Application of epigenetics in aquaculture**

**Table 2.** Growth and performance traits for different crustacean species.

Body appearance traits identified include the red body colour excluding normal black pigmen‐ tation in tilapia [168], silvery skin with few spots in rainbow trout [169], albinism in rainbow trout [170] and melanization in threespine sticklebacks (*Gasterosteus aculeatus*) [171]. Genetic traits essential for improving production in fish farming include traits for feed conversion ratio [172], robustness [173], maturation timing [174], cold tolerance [163, 175], high temperature tolerance [176] and salinity tolerance. In anadromous species such as Atlantic salmon, genetic traits for smoltification [177], migration and spawning timing [178] have been determined.

#### **5.2. Disease resistance and susceptibility traits**

The rapid expansion of aquaculture to become one of the leading sources of protein in the world has brought with it an increase in infectious diseases in aquaculture. To reduce the disease burden and prevent the use of antibiotics, which have been shown to have adverse environ‐ mental effects, there has been a tremendous increase in genomics studies aimed at identify‐ ing disease resistance traits in different cultured organisms. And as such, different approaches such as SNP, MTLS, AFLP, RAPD, RFLP and QTL analyses have been used for the iden‐ tification of disease resistance and susceptibility traits in different aquatic organisms. In the case of fish viral diseases, QTL resistance traits have been generated for grass cap reo‐ virus (GCRV) infection in grass carp [179], nervous necrosis virus (NNV) in seabass [180], viral hemorrhagic septicemia (VHS) in turbot [181] and rainbow trout [182], infectious salmon anaemia (ISAV) virus in Atlantic salmon, lymphocytic disease virus in Japanese flounder [183] and infectious pancreatic necrosis virus (IPNV) in Atlantic salmon [184, 185]. Among these, the QTL for resistance against IPNV has contributed to significantly reducing the IPNV incidence by >80% from 2008 when IPNV resistance fish were introduced in the Norwegian Atlantic salmon indus‐ try to 2015 [186]. Bacteria disease for which QTL resistance traits have been identified include coldwater disease in rainbow trout [187], *Aeromonas hydrophila* in rohu (*Labeo rohita*) [188], *Vibrio anguillarum* in Japanese flounder [189], *Flavobacterium psychrophilum* in rainbow trout [190] and pastuerellosis in Gilhead seabream [191]. As for parasitic diseases, QTL resistance traits have been identified for *Gyrodactylus salaris* in Atlantic salmon [192] and Monohenean parasite (*Benedenia seriolae*) in Yellow tail (*Seriola quinqueradiata*) [193].

In shrimps, resistance traits have been identified for white spot syndrome virus (WSSV) in Indian black tiger shrimp (*Penaeus monodon*) [194, 195], Fenneropenaeus (*Penaeus chinensis*), infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance in shrimp (*Litopenaeus stylirostris*) [196] and taura syndrome resistance in Pacific white shrimp (*P. van‐ namei*) [197]. Among these, the QTL for resistance against TSV has contributed to significant reduction of the disease prevalence in shrimps by generating pathogen‐specific free disease shrimps for us in breeding programmes in aquaculture.
