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After DNA barcoding, with the advances of Genomics approaches, in the last
decade, many important issues in conservation have been best explored for different
organisms. Within Genomics, Next-generation Sequencing (NGS) opened up the possibility of working with thousands of molecular markers, even for little-known species.
The low cost of NGS, when compared with the amount of data generated by traditional
sequencing, has made this technology feasible to widely access the species genome.
Genomic studies focusing on Epinephelus itajara were not developed yet.
However some researches can be mentioned for the genus. Complete mitochondrial
genomes of other Epinephelus species were published (Qu et al. 2012; Wang et al.
2016; Wu et al. 2015; Yang et al. 2016).
Zhuang et al. (2013) characterized and compared genomes among 22 groupers
species of the family Epinephelidae. Three distinct genome organizations were
identified, two of them never previously reported in vertebrates. With this study the
authors provide further support for the elevation of the subfamily Epinephelinae to
family Epinephelidae; the resurrection of the genus Hyporthodus; and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus,
and Aethaloperca to genus Cephalopholis.
Yu et al. (2016) identified 264,072 raw SNPs (single-nucleotide polymorphisms)
by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides). They determined a map containing 24 linkage groups
(LGs) with a total genetic distance of 1231.98 cM. Twenty-seven significant growthrelated QTLs were identified and 17 genes, including three that have been considered to be involved in fish growth. The authors consider that these QTLs will be
useful in marker-assisted selection (MAS) efforts to improve growth-related traits in
this economically important fish.
NGS has been considered a very promising advance not only for genetic breeding, but also to answer relevant biological issues in Conservation Genetics.
One good example of discussion about the NGS applications for marine systems
comes from Willete et al. (2014), that organized questions mainly into two general
categories: (1) population genomics, and (2) local adaptation and demographic history of marine organisms. Some of those questions we can point out as really important for future genetic studies of Epinephelus itajara: (a) Is it possible to assess the
population structure and genetic variability at a level that can guide a restoration of
local stocks?, (b) How might we estimate population size of marine organisms?, (c)
How will marine organisms respond to environmental stress, particularly those
related to climate change?, and (d) How to infer the spatial connectivity of important commercially populations or threatened species, and how can this support positioning of Fisheries Management Zones (FMZ) or Marine Protected Areas (MPAs)?
Concluding, despite of advances in Epinephelus itajara genetics there is still
much to do. Data including individuals from different localities and evaluation of
more traditional molecular markers associated to next generation sequencing are
necessary to figure out more conclusive structure and phylogeography, as well as
provide better access to its genome and understanding about the adaptive processes
in which the species is involved.
14 The Atlantic Goliath Grouper: Conservation Strategies for a Critically Endangered…
After DNA barcoding, with the advances of Genomics approaches, in the last
decade, many important issues in conservation have been best explored for different
organisms. Within Genomics, Next-generation Sequencing (NGS) opened up the possibility of working with thousands of molecular markers, even for little-known species.
The low cost of NGS, when compared with the amount of data generated by traditional
sequencing, has made this technology feasible to widely access the species genome.
Genomic studies focusing on Epinephelus itajara were not developed yet.
However some researches can be mentioned for the genus. Complete mitochondrial
genomes of other Epinephelus species were published (Qu et al. 2012; Wang et al.
2016; Wu et al. 2015; Yang et al. 2016).
Zhuang et al. (2013) characterized and compared genomes among 22 groupers
species of the family Epinephelidae. Three distinct genome organizations were
identified, two of them never previously reported in vertebrates. With this study the
authors provide further support for the elevation of the subfamily Epinephelinae to
family Epinephelidae; the resurrection of the genus Hyporthodus; and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus,
and Aethaloperca to genus Cephalopholis.
Yu et al. (2016) identified 264,072 raw SNPs (single-nucleotide polymorphisms)
by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides). They determined a map containing 24 linkage groups
(LGs) with a total genetic distance of 1231.98 cM. Twenty-seven significant growthrelated QTLs were identified and 17 genes, including three that have been considered to be involved in fish growth. The authors consider that these QTLs will be
useful in marker-assisted selection (MAS) efforts to improve growth-related traits in
this economically important fish.
NGS has been considered a very promising advance not only for genetic breeding, but also to answer relevant biological issues in Conservation Genetics.
One good example of discussion about the NGS applications for marine systems
comes from Willete et al. (2014), that organized questions mainly into two general
categories: (1) population genomics, and (2) local adaptation and demographic history of marine organisms. Some of those questions we can point out as really important for future genetic studies of Epinephelus itajara: (a) Is it possible to assess the
population structure and genetic variability at a level that can guide a restoration of
local stocks?, (b) How might we estimate population size of marine organisms?, (c)
How will marine organisms respond to environmental stress, particularly those
related to climate change?, and (d) How to infer the spatial connectivity of important commercially populations or threatened species, and how can this support positioning of Fisheries Management Zones (FMZ) or Marine Protected Areas (MPAs)?
Concluding, despite of advances in Epinephelus itajara genetics there is still
much to do. Data including individuals from different localities and evaluation of
more traditional molecular markers associated to next generation sequencing are
necessary to figure out more conclusive structure and phylogeography, as well as
provide better access to its genome and understanding about the adaptive processes
in which the species is involved.
14 The Atlantic Goliath Grouper: Conservation Strategies for a Critically Endangered…