Characterization of ten polymorphic microsatellite loci useful for selective breeding program in Indian White shrimp Fenneropenaeus indicus

A selective breeding program was designed to select for disease resistance and growth in marine shrimp in Egypt. The project identified a number of polymorphic microsatellite markers to trace pedigrees and apply marker-assisted selection (MAS) in the current shrimp breeding program in Egypt. The project succeeded to isolate and characterize microsatellite genetic markers for the Indian white shrimp Fenneropenaeus indicus and trace the pedigree of different families from the breeding program. Microsatellite markers and pedigree were both used to assess genetic variability and effective population size. Using 10 loci, selected shrimp populations for three generations showed a decline in the expected heterozygosity (15 percent) and allelic diversity indices (52 to 93 percent), compared to the wild population (P < 0.05). Effective population size estimates based on microsatellites declined from 46.5 to 77.0 percent in cultured populations (P < 0.05), compared to the wild population. Working in direct contact with stakeholders has led to improvement in dissemination of the knowledge and awareness. Our strategy to control long-term inbreeding in breeding program is to use a relatively large number of broodstock in each generation, and to control mating among relatives by imposing mating restrictions (use of microsatellite markers for paternity analysis and mate design). The results have shown that the use of microsatellite markers suggest that heterozygosity at microsatellites loci is well correlated with individual inbreeding coefficients. The decline of genetic variability in the cultured selected population due to domestication, and evidence of a further smaller decline in effective population size across generations in the selected population, was observed when analyzing pedigree and microsatellite data. Pedigree keeping is required to prevent the decline of effective population size and maintain genetic variability in shrimp breeding programs, while microsatellites are useful to assess effective population size changes at the population level. However, we still allow preservation of the genetic variation necessary to continue improving the population for current traits or others that may need to be incorporated in the future. This work was supported by Science & Technology Development Fund (STDF), Egypt under grant no. 5661.

Keywords: Indian white shrimp, Fenneropenaeus indicus, selection, disease selection, resistance, breeding program, genetic improvement, shrimp diseases, WSSV, IHHNV, YHV, vibrio, EMS (AHPND), breeding nucleus, genotyping system, polymorphism, microsatellite markers, primers, inbreeding, pedigree, allele frequencies, full-sib family, intellectual property.