Levels of genetic diversity and inferred origins of Penaeus vannamei culture resources in China: Implications for the production of a broad synthetic base population for genetic improvement

Highlights • Despite the most important role of Penaeus vannamei in shrimp aquaculture, population genetics information for broodstock from either domesticated or wild population is limited; in this paper we report on genetic (microsatellite) variation for this important culture species captured in 36 Chinese breeding lines from 22 hatcheries which is the most comprehensive sampling design to our knowledge. • Microsatellite data analysis successfully resolved different origins of P. vannamei culture stocks used in China that resulted in the detection of four lineages with genetically diverse origins. • Results of the analysis here has provided the foundation and guidelines to develop a base line for genetic improvement program with optimal levels of genetic variation and a relatively low inbreeding coefficient. • We believe that the data presented here clearly demonstrate the utility of accessing genetic resources from a variety of sources (particularly when natural populations are not available) and show this as a viable and necessary first step for developing a base population for pursuing subsequent genetic improvement in alien aquaculture species. Abstract Knowledge about the origins and relative levels of genetic variation available in domesticated strains can be used to develop robust synthetic populations for use in stock improvement programs, in particular, where wild stocks are unavailable or the target species is alien. Here, we undertook a case study of Pacific white shrimp (Penaeus vannamei) where we utilised neutral molecular genetic variation data, population structure, and genetic relatedness as an initial step towards producing a base line for a long-term family-selection breeding program in China. The objective was to capture and maximise genetic variation in the base population while at the same-time to control inbreeding levels. Genetic diversity in 1162 individuals from 36 breeding lines sourced from 22 hatcheries with domesticated broodstock available in China was assessed using seven microsatellite loci. Genetic diversity levels in the sampled lines were considered to be healthy, with a mean number of alleles (A) 5.85, ranging from 4.00 in B4 to 12.43 in T1, and mean allelic richness (Ar) 4.46, ranging from 3.35 in B4 to 6.69 in T1 breeds. Mean inbreeding coefficient (Fis) was 0.07 among the 36 lines indicating acceptable levels of inbreeding. Genetic differentiation between lines from different hatcheries was moderate, with a mean FST estimate of 0.09 among all pairs of hatchery lines. Bayesian assignment and phylogenetic analyses indicated that hatchery lines in China could be broadly divided into four groups: i) a line from North America (NA1), originally sourced from Mexico (north Sinaloa) and Ecuador, ii) two representatives of the Kona line developed in Hawaii (Oceanic Institute) (NA2,3), iii) a line developed in Thailand (Southeast Asia 1 (SA1)), and iv) a mixed group containing stocks that originated in Latin America (predominantly from Panama and Colombia) (LA; SA2; CN1,2; NA4,5). From these data, we argue that a complete 4 × 4 diallel cross (16 crosses) of the four subpopulations should be trialled in China to develop a base line for a family selection breeding program with optimal levels of genetic variation and a relatively low inbreeding coefficient