Atal did his thesis on parentage analysis in tilapia

Thesis title

Parentage analysis in Nile tilapia with two types of DNA-markers

Summary

Molecular pedigree is an effective tool to assure correct parentage in a selective fish breeding program. Although microsatellites are commonly used for this purpose, SNPs are getting more common because of their higher abundance and low cost. The objective of the present study is to re-construct the family pedigree of the selected Nile tilapia individuals using microsatellite and SNP markers and to estimate the best marker type for these studies. Twelve microsatellites and 289 (first run), 148 (second run) SNP loci were studied in the 10th and 11th generation of Genetically Improved Farmed Tilapia (GIFT) population. In total, 384 fish placed in 4 different hapas were analysed using the computer allocation programs PAPA 2.0, Cervus 3.0 and Colony 2.

Cervus achieved 100% allocation in all the cases, for PAPA, the allocation rates were 96.88%, 100%, 99.82% and 95.56% in the 4 hapas using microsatellites. For all the hapas, Colony could not allocate a significant portion of animals. While comparing allocation results from different computer programs, PAPA and Cervus gave the highest concordance in the allocation as 83.23%, 86%, 82.5% and 82.22% for 4 different hapas respectively using microsatellites but SNPs gave a very different result. The accuracy of the parental allocation of this study could not be justified in absence of a standard. But, because of the big difference in the allocation by microsatellites and SNPs, it seems that not all actual parents were genotyped for the study which should be ensured first. Reasonably, the best marker type could not be estimated. However, the study suggests not to rely on only one computer program for the parental allocation, but rather use programs based on both likelihood and exclusion probability.