Transcriptome analysis of the gonad reveals growth differences between large, medium and small individuals in a pure family of Macrobrachium rosenbergii

Macrobrachium rosenbergii is one of the most economically important crustacean species worldwide because of its nutritional value and good meat quality. There are obvious growth differences between individuals of M. rosenbergii; however, the exact mechanism underlying these growth differences remains unclear. Herein, we first measured the phenotypic traits of M. rosenbergii and analyzed the correlations among them. Furthermore, next-generation sequencing was employed to determine the transcriptome differences between different sized individuals of M. rosenbergii. Many differentially expressed genes (DEGs) related to growth were identified and subsequently verified using quantitative real-time reverse transcription PCR. A relationship model between phenotypic traits and DEGs of M. rosenbergii was established, which will provide useful information for molecular assisted selection in genetic improvement. In addition, weighted gene co-expression network analyses was conducted, and the purple module was identified to have the highest correlation coefficient with the palm length. Gene ontology functional enrichment analysis showed that the DEGs from different sized M. rosenbergii participated in different biological functions. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that DEGs of males were mainly enriched in actin cytoskeleton regulation, starch and sucrose metabolism, apoptosis, and unsaturated fatty acid biosynthesis; whereas the DEGs of females were mainly enriched in glutathione metabolism, starch and sucrose metabolism, galactose metabolism, lysosome, animal mitosis, and other pathways. The results revealed the molecular mechanism of the growth differences of M. rosenbergii and established a relationship model between phenotypic traits and key genes, which will provide important support for the genomic selection and genetic improvement of traits in M. rosenbergii during modern breeding.