Open Access Research article

Insights into food preference in hybrid F1 of Siniperca chuatsi (♀) × Siniperca scherzeri (♂) mandarin fish through transcriptome analysis

Shan He1, Xu-Fang Liang1*, Jian Sun1, Ling Li1, Ying Yu1, Wei Huang1, Chun-Mei Qu1, Liang Cao1, Xiao-Li Bai1 and Ya-Xiong Tao2

Author Affiliations

1 Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, Wuhan 430070, PR China

2 Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849-5519, USA

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BMC Genomics 2013, 14:601  doi:10.1186/1471-2164-14-601

Published: 5 September 2013



As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Mandarin fish accept only live prey fish and refuse dead prey fish or artificial diets. Very little is currently known about the genes regulating this unique food preference.


Using transcriptome sequencing and digital gene expression profiling, we identified 1,986 and 4,526 differentially expressed genes in feeders and nonfeeders of dead prey fish, respectively. Up-regulation of Crbp, Rgr and Rdh8, and down-regulation of Gc expression, consistent with greater visual ability in feeders, could promote positive phototaxis. Altered expressions of period, casein kinase and Rev-erbα might reset circadian phase. Down-regulation of orexigenic and up-regulation of anorexigenic genes in feeders were associated with lower appetite. The mRNA levels of Creb, c-fos, C/EBP, zif268, Bdnf and Syt were dramatically decreased in feeders, which might result in significant deficiency in memory retention of its natural food preference (live prey fish). There were roughly 100 times more potential SNPs in feeders than in nonfeeders.


In summary, differential expression in the genes identified shed new light on why mandarin fish only feed on live prey fish, with pathways regulating retinal photosensitivity, circadian rhythm, appetite control, learning and memory involved. We also found dramatic difference in SNP abundance in feeders vs nonfeeders. These differences together might account for the different food preferences. Elucidating the genes regulating the unique food preference (live prey fish) in mandarin fish could lead to a better understanding of mechanisms controlling food preference in animals, including mammals.

Food preference; Live prey fish; Mandarin fish; Transcriptome sequencing; Digital gene expression