Recent advances of genome mapping and marker‐assisted selection in aquaculture

Abstract

Aquaculture is the fastest growing sector in agriculture. Substantial genetic gains have been achieved in a few cultured species using conventional selective breeding approaches. However, the majority of fish and shellfish species remain in their wild state. Due to the recognition of the enormous potential of marker‐assisted selection (MAS) to speed up genetic gain through early selection, aquaculture scientists have constructed linkage maps in over 40 species and mapped quantitative trait loci (QTL) for important traits in over 20 species since the 1990s. Although MAS and genomic selection (GS) have not been widely used in aquaculture, their application in breeding programmes is expected to be a fertile area of research. In this paper, I summarized the recent advances of linkage and QTL mapping, as well as MAS in aquaculture species. I also discussed the potentials of genome‐wide association studies (GWAS) and GS in aquaculture species.

Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species

“…A genetic linkage map with many DNA markers is needed to efficiently find markers associated with quantitative trait loci (QTL) that can be used in marker-assisted selection breeding programs to genetically improve traits, such as disease resistance, high growth rate, and sex determination in Pacific bluefin tuna seed and seedlings. QTL analyses [50] for specific traits have been performed in many fish including groups phylogenetically close to Pacific bluefin tuna in Percomorpha, such as two yellowtail species (Seriola quinqueradiata and Seriola lalandi) in Carangidae [37] [51] and Japanese flounder (Paralichthys olivaceus) and Atlantic halibut (Hippoglossus hippoglossus) in Pleuronectiformes [45] [52] [53]. In this study, we developed sex-specific linkage maps using a tuna draft genome sequence.…”

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

“…Economic traits in aquaculture fish, especially growth-related quantitative traits, are the main goals for improvement in a genetic breeding program. Growth-related traits have been measured and reported in several economically important marine fishes (Yue 2013). To study growth-related traits in fish and other species by molecular tools is complex, because growthrelated traits are influenced not only by genetics, but also by the environment (Abraham et al 2007;Molano et al 2011).…”

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“…Growth is a quantitative trait, under polygenic control, with the most important influence on the somatotropic axis and myogenic transforming growth factor superfamily (Valente et al, 2013;Yue, 2013). Identification of the major quantitative trait loci (QTLs) or genes affecting growth is performed usually by linkage map construction and QTL mapping or in association studies and candidate gene approaches (De-Santis & Jerry, 2007;Yue, 2013).…”

“…Identification of the major quantitative trait loci (QTLs) or genes affecting growth is performed usually by linkage map construction and QTL mapping or in association studies and candidate gene approaches (De-Santis & Jerry, 2007;Yue, 2013). Heritability of growth is usually moderate to high (h 2 =0.2 to 0.7), resulting in correlations of growth rates between closely related individuals (Ma, Wang & Lei, 2009).…”