Integrated Genomic, Transcriptomic and Metabolomic Analyses Identify Key Genetic Determinants and Regulatory Networks...

Salinity stress severely restricts the culture and geographical expansion of Macrobrachium rosenbergii. Artificial selective breeding has generated a salt-tolerant (NY) strain that can survive and grow normally under 10‰ salinity, while the commercial Suhu No.1 (SH) strain and commercial population (PT) exhibit weaker salt adaptability. In the present study, we performed whole-genome resequencing, transcriptome and untargeted metabolomic analyses to systematically reveal the molecular basis of salinity tolerance in the NY strain. Population genetic analyses including ADMIXTURE, PCA and phylogenetic tree demonstrated obvious genetic differentiation among NY, SH and PT populations, and genome-wide Fst scanning screened candidate genes mainly enriched in ion transport, osmotic regulation and energy metabolism pathways. Transcriptomic analysis identified 156 differentially expressed genes (DEGs) between NY and SH strains, with principal component analysis showing clear inter-group separation. Functional enrichment indicated that DEGs were predominantly involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, autophagy and cellular homeostasis. qRT-PCR validation confirmed the reliability of transcriptome expression patterns of key salt-tolerance genes such as NKA, NHX, TPS and HSP70. Untargeted metabolomics identified a total of 1079 metabolites and 69 differentially accumulated metabolites (DAMs). DAMs were significantly enriched in starch and sucrose metabolism, phosphotransferase system (PTS) and ABC transporters under both positive and negative ion modes. Integrated transcriptomic and metabolomic analysis revealed 9 shared KEGG pathways in positive ion mode and 14 in negative ion mode, and key genes and metabolites displayed coordinated variation in carbohydrate metabolism, transmembrane transport and osmotic adjustment. Collectively, the NY strain achieves strong salinity tolerance by integrating genetic variation, transcriptional reprogramming and metabolic remodeling, synergistically maintaining ion homeostasis, osmotic balance and energy supply. This study provides important genetic resources and a theoretical framework for molecular breeding and salinity adaptation mechanism research of M. rosenbergii.