Abstract: 【Objective】To identify differentially expressed genes(DEGs)between small and large individuals of Maccullochella peelii,to provide a scientific basis for the deep study of genes related to growth and development,molecular genetics and breeding.【Method】Significantly large and small M. peelii individuals obtained under the same breeding conditions were selected and their muscle tissue sampled to construct cDNA libraries. Transcriptome sequencing of M. peelii muscle tissues was conducted using the Illumina HiSeq^TM 4000 sequencing platform. The obtained unigenes were compared in Nr,Nt,Pfam,KOG/COG,Swiss-Prot,KEGG and GO databases. The differentially expressed genes were screened using FPKM and DEGseq. GOseq and KOBAS were used to perform GO function annotation and KEGG signaling pathway enrichment,then identified by SSR by MISA.ResultsA total of 39749 unigenes were generated from muscle tissue of M. peelii,with lengths ranging from 301 to 55230 bp and an average length of 1705 bp. There were 27046, 20824,18268 and 17772 unigenes annotated to Nt,Nr,Swiss-Prot and Pfam databases,respectively. In total,6742 unigenes were annotated by seven databases,accounted for 16.96% of the total unigenes. Differentially expressed genes were defined as those displaying an adjusted P<0.05 and|log₂ Fold Change|>1. A total of 722 DEGs were selected,consisting of 308 up-regulated genes and 414 down-regulated genes. The results of GO function annotation showed that the GO function items with a large number of annotation genes including cellular process,metabolic process,membrane, organelle and binding. KEGG signaling pathway enrichment revealed that DEGs were enriched in 234 signal pathways, mainly involving phosphatidylinositol 3 kinase/protein kinase signal pathway,MAPK signal pathway,insulin signal pathway and the FoxO signal pathway. A total of 22120 SSRs were identified from 39749 unigenes,accounted for 55.65% of the total number of unigenes. The average spacing of SSRs was 3063 bp.【Conclusion】The obtained DEGs in M. peelii muscle tissue based on transcriptome sequencing mainly play the functions of binding,cellular process and metabolic process,and mainly enriched in PI3K Akt signal pathway,ribosomal signal pathway,FoxO signal pathway,apoptosis and other energy metabolism related pathways,which together regulate the growth and development of M. peelii.