Paternity assignment of pacific white shrimp (Litopenaeus vannamei) using microsatellite DNA markers

Abstract

Pacific white shrimp, Litopenaeus vannamei, is the most economically important shrimp species cultured worldwide, constituting 60% of global shrimp production. L. vannamei has been selectively bred for commercially valuable traits such as high growth rate, survival rate, hatchery rate, and disease resistance. However, selectively bred shrimp populations are susceptible to inbreeding, resulting in reduction in phenotypic performance. To mitigate the problems of inbreeding depression, it is necessary to establish and maintain reliable shrimp pedigree for the proper management of broodstock in selective breeding programs. Microsatellite DNA markers have been indicated as the most effective genetic tool for paternity assignment in shrimp, as physical tagging and internal markers are impractical. Characteristics that contribute to microsatellite's effectiveness in paternity determination include its high variability and heritability, co-dominant alleles, its ubiquitous presence in the genome, and ease of genotyping. The main objective of this research is to determine the paternity of 9 families of shrimp progeny using 7 species-specific microsatellite DNA markers, Pvan 0013, Pvan 1003, Pvan 1758, Pvan 1815, M1, TUGAPv 7-9.115, and TUGAPv 7-9.132. These microsatellites were amplified via multiplex PCR and were genotyped using an automated DNA sequencer. The raw genotyping results were analyzed and scored using the GeneMarker software. Allelic frequencies, computed simulations and paternity analysis were done using CERVUS. All but one microsatellite marker M1 were highly polymorphic with Polymorphic Information Content (PIC) and expected heterozygosities above 0.5, and consist of more than 4 alleles. Computer simulations suggested that assignment success rate is highly dependent on the number of loci, with assignment success of 99% when 7 loci were used in combination. However, the assignment success rate for the actual paternity analysis was only 90%, as a result of genotyping errors and the presence of null alleles.