Genetic diversity and population structure of a giant freshwater prawn (Macrobrachium rosenbergii) breeding nucleus in China

The giant freshwater prawn breeding programme in China has been carried out as a closed nucleus from 2006. The programme aimed to improve the harvest body weight and pond survival and has achieved remarkable progress. In this study, the genetic diversity and population structure of the giant freshwater prawn breeding nucleus was analysed. Pedigree completeness, the status of genetic diversity, inbreeding accumulation and effective population size of the breeding nucleus were analysed according to the pedigree record. From 2006 to 2014, a total of 107,941 individuals with 555 males and 967 females in nine generations were included in the analyses. Pedigree completeness index in six generations was at least 0.92. After performing eight selections, the genetic diversity decreased by 3%, 67% of which was caused by random genetic drift. After performing 2 years’ selection, the inbreeding level began to show a marked upward trend. The regression of the average rate of inbreeding and the average rate of co‐ancestry was 0.0041 and 0.0051 from 2006 to 2014. The effective population size calculated from the above two parameters was 122 and 98 respectively. The effective population size is still within the recommended level for a population to continue the genetic improvement programme, but below the level required (500) for retaining the evolutionary potential. To restrain the increasing level of inbreeding and maintain effective population size, measures are required to develop a breeding programme which integrates management of genetic variability and selection.