Comprehensive evaluation of germplasm resources of nine Macrobrachium rosenbergii strains in China

Abstract

Macrobrachium rosenbergii, as an introduced species, is extensively cultured in China. In this study, 176 individuals from nine domestic strains in China, i.e., Florida (FD), Guangxi (GX), Hefu (HF), Myanmar (MD), “Nantaihu No. 2″ (NT), Thailand (TG), Taiwan (TW), “Shufeng No. 1″ (SF), and Zhengda (ZD), were collectedfor genome resequencing. We evaluated the genetic diversity, population structure and population history of nine cultured strains using SNP markers. We found that genetic diversity of the M. rosenbergii strains was at a low level, among which FD and TG strains showed relatively higher genetic diversity, inferring that the genetic diversity of domestic populations decreased after artificial selection. Population genetic structure analysis showed that the individuals GX, HF, SF and NT strains were irregularly clustered together, and the ZD and TW strains exhibited the specific ancestors compared with other strains. The phylogenetic tree revealed that the individuals from TW, MD, ZD strains grouped into population-specific clusters. The principal components analysis (PCA) also showed that the nine strains were mixed together except the individuals from ZD and TW strains which were separated into specific subgroups. The Fst analysis showed that the Fst values detected from nine strains were less than 0.05, with the lowest Fst observed between SF and NT strains. In addition, two positively selected genes involved in metal transport and stress response were identified in the nine domestic strains by using selective sweep analyses with composite likelihood ratio (CLR), Fst, Pi, and Tajima’ D methods. The TreeMix phylogeny inferred four gene flow events among the nine strains, which occurred in the following directions: (1) from the common ancestor of ZD and TG to SF, (2) from SF to MD, (3) from SF to NT, and (4) from HF to GX. This study contributes to the better understanding genetic background and germplasm status of domestic M. rosenbergii strains in China.