4.4 Targeted artificial selection during domestication ofF. chinensis
Domestication of animals was driven by both natural and artificial selection. Under these directed selection pressures, change in the allele frequency in specific regions may be accumulated in the animal genome after domesticated for several generations (Nielsen, Hellmann, Hubisz, Bustamante, & Clark, 2007). The cultured shrimps were derived from the wild population by continuous, high-intensity artificial selection for growth traits and is characterized by faster growth and higher body weight than wild individuals. Genes responsible for these characteristics may be detected by identifying unique selection signatures in the genome. Selection signature is characterized by the decrease in polymorphism and increase in linkage disequilibrium in certain loci. Identification of genetic variations by selection signature reveals the genetic mechanism of the formation of phenotypic trait diversity during selection (Lopez, Neira, & Yanez, 2014). In the present study, most genes with selection signatures were identified to participate in metabolic processes. Metabolism is the basis of growth and is related to growth rate (Krieger, 1978; Vahl, 1984). The changes in the allele frequency of genes related to metabolic processes suggest artificial selection on growth. However, owing to the short history of shrimp domestication, the genetic divergence between the wild and cultured shrimp populations is not significant.
A pathway named the phototransduction-fly pathway was enriched by genes with selection signatures; of the 27 background genes of this pathway, six genes were located in the selection signature regions. This enriched pathway signifies a visual change in domesticated shrimp.Fenneropenaeus chinensis juveniles exhibit an intense attack behavior (P. Zhang, Zhang, Li, & Meng, 2008). We propose that the high-density culture environment required them to develop better vision to survive cannibalism.
Among the pathways enriched by the candidate genes, there was a pathway related to the nervous system, neuroactive ligand-receptor interaction pathway, which suggests that genes affecting neuronal development were also targeted during domestication. Animal behavior is regulated by the nervous system. Compared with aggressive animals, docile animals survive more easily in a culture environment (Carneiro et al., 2014; Darwin, 1860). We speculate that tame shrimps were selected for during domestication, and therefore the related genes were targeted.