Genome resequencing reveals genetic status of Macrobrachium rosenbergii populations in China

The giant freshwater prawn (Macrobrachium rosenbergii) has been widely cultured in China since 1990s. In this study, 189 individuals were sampled from 10 distinct populations, including original populations introduced from abroad and domesticated strains in China, namely Florida (FD), "Nantaihu No.2" (NT), Vietnam (YN), Sri Lanka (SK), Bangladesh (ML), Thailand (TG), Taiwan (TW), "Shufeng No.1" (SF), Zhengda (ZD) and New Myanmar (NMD). The genetic diversity and population structure of these populations were analyzed based on a dataset of 300,828 genome-wide SNP loci. The population structure analysis showed that the 10 populations shared 4 ancestors, and the domestic populations (i.e., SF, ZD, TW and NT) shared a common ancestor. The phylogenetic analysis showed that the 10 populations were grouped into 4 branches, with all the domestic populations clustering together. Estimation of fixation index (Fst) values revealed relatively lower Fst values among the domestic populations, in contrast to the more significant differences observed between domestic and foreign-origin populations. Gene flow analysis revealed three significant events of genetic exchange among the 10 populations: (1) from YN to the common ancestor of FD, TG and the domestic populations, (2) from NMD to the common ancestor of TG and FD, and (3) from the common ancestor of NMD, YN, ML and SK to ZD population. In addition, selective sweep analysis, utilizing Fst and nucleotide diversity (Pi) estimations, was conducted on representative populations (i.e., ML and SF), and 7 positively selected genes were identified, including Prospero Homeobox 1 (Prox1), Forkhead Box L1 (Foxl1), Tousled Like Kinase 2 (TLK2), G Protein Subunit Alpha 14 (Gna14), Uronyl 2-sulfotransferase (Ust), MAX Network Transcriptional Repressor (Mnt) and Importin-9 (Ipo9). These findings contribute to elucidating the breeding potential of the introduced populations and provide insights into the genetic status of the domestic breeding strains of M. rosenbergii in China. •The genetic diversity of domestic populations was lower than that of original populations.•Seven positive genes related to local immunity, cell cycle regulation and retinal formation were detected.•Three gene flow events were found among the 10 populations.