Network‐based quantitative proteomics identified significant proteins associated with growth heterosis in triploid fish

Abstract

Triploid fish show significant growth heterosis compared to their parents, but its underlying molecular mechanisms are still largely unknown. In this study, Sequential Window Acquisition of All Theoretical Mass Spectra-based quantitative proteomic profiling was performed on the liver tissues from triploid crucian carp (TCC) and its parents red crucian carp (RCC) and allotetraploid (4nAT). Comparative proteomics analysis revealed that several causal proteins were differentially regulated between TCC and its parents. Particularly, proteins eno3 (p = 1.18E-3, ratio = 2.86 between TCC and RCC; p = 4.76E-4, ratio = 4.92 between TCC and 4nAT) and glud1a (p = 4.4E-7, ratio = 9.21 between TCC and RCC; p = 7.59E-7, ratio = 4.57 between TCC and 4nAT) were significantly upregulated in triploid fish. Multiple bioinformatics analysis including functional enrichment, pathway analysis and protein–protein interaction network construction further suggested that these candidate proteins play crucial roles in regulating growth heterosis by mediating important metabolic pathways including ‘carbohydrate metabolic process’, ‘glycolytic process’ and ‘glycolysis/gluconeogenesis’ and ‘carbon metabolism’. They may accelerate the processes of substrate and energy metabolism to meet the requirement of body growth. The identified candidate proteins such as eno3, glud1a in this study may serve as significant target indicators for further research involved in hybrid breeding and variety improvement.