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Inbreeding and disease outbreaks in farmed shrimp in Egypt: Evidence from microsatellite markers  

Mohamed E. Megahed
National Institute of Oceanography and Fisheries, Gulfs of Suez & Aqaba's branch, Suez, Egypt

The objective of this study was to estimate the decline of genetic variability and the changes in effective population size in shrimp breedung program after three generations of selection for disease resistance and growth. Without a doubt, the disease crisis facing shrimp farming in Egypt nowadays is a result of interaction between management practices that cause inbreeding, and the susceptibility to disease and environmental stresses. The increase of inbreeding has increased the incidence of WSSV, IHHNV, YHV, vibrio and EMS (AHPND). In 2013 a breeding program for selection of disease resistant shrimp Fenneropenaeus indicus started in Egypt as an applied commercial breeding program to improve production and profitability in shrimp aquaculture. Two problems faced the current breeding program. 1) However, because of selection programs implies that only a portion of the population contributes genes that are transmitted to the next generation, reducing effective population sizes. 2) The shrimp farmers are mating relative shrimp and using inbred lines. This increased the degree of inbreeding over generations. The increase of the inbreeding has been noticed in the traits of productive interest such disease resistance, growth are and reproductive performance. Therefore, in our breeding program for disease resistance and growth in shrimp F. indicus we are regularly monitor and quantify the effects of inbreeding and proper balancing of the response to selection and the effects of inbreeding.

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%) and allelic diversity indices (52 to 93 %) compared to the wild population (P < 0.05). Effective population size estimates based on microsatellites declined from 46.5 to 77.0 % in cultured populations (P < 0.05) compared to the wild population. However, 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 control mating among relatives by imposing mating restrictions (use of microsatellite markers for paternity analysis and mate design). The results showed that 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 were 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.

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