Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp

Abstract

Abstract The grass carp (Ctenopharyngodon idella) is the most productive freshwater fish in the world. However, little is known about the functional genes and genetic regulatory systems that control its growth traits. In this study, we used two superior grass carp parents with fast-growing offspring and two inferior grass carp parents with slow-growing offspring to create three grass carp families, namely, the superior-superior family (SS), the inferior-inferior family (II) and the superior-inferior family (SI). The average body weight of the offspring of these families showed a stable ranking (SS > SI > II) under the satiation and starvation feeding modes. Then, the transcriptomes of the brain and the hepatopancreas of grass carp with different growth rates were obtained for each family, and it was found that the number of differentially expressed genes (DEGs) in the different organs showed family specificity. The DEGs were mainly found in the hepatopancreas of SS and the whole brain of II, while they were more balanced in SI. There were 14 common DEGs among the three families, including 3 negatively correlated genes (ahsg2, lect2 and drd5) and 11 positively correlated genes (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3, fabp7 and endod1). Deleting ahsg2 in zebrafish significantly increased the upper limit of individual body weight during the experiment, but only slightly increased the average growth rate of the population. In addition, we analyzed the SNP in each family and preliminarily analyzed the potential genetic mechanisms of family-specific regulation of growth traits. This study revealed for the first time the family specificity of the growth regulation mechanism of grass carp at the transcriptional level, verified the function of a growth negative regulatory gene ahsg2, and further analyzed the possible molecular mechanism of growth differences among different families. This study provides new insights into the genetic regulation mechanism of grass carp growth.