Title of the Thesis: Genotypic Characterization of Ardi Goat using Microsatellite Markers

Name of Researcher: Muhamed Muneeb Muhamed Musthafa

University: King Saud University
College: Food & Agricultural Sciences
Department: Animal Production
Branch/Track: Animal Genetics
Degree: MSc in Animal Production
Date of Discussion: 2011-02-22 G/ 1432-03-19 H

Abstract:

Genetic Characterization is an important step for maintaining genetic variability of populations which could help in planning for conservation strategies and genetic improvement. No recent studies were found regarding genotypic variability of Saudi Arabian goat populations. Therefore, the main focus of this study was to measure the genetic diversity of Ardi goat breed found in Riyadh region. Blood samples were collected from 43 unrelated animals found in 11 different herds. DNA was extracted using GFX genomic kit. PCR was performed using 14 microsatellite markers recommended by ISAG/FAO. PCR products were run on 2% Agarose gel and were mixed based on their fluorescent dyes and sizes. Fragment analysis was carried by ABI Prism genetic analyzer 3130. Microsatellite fragment sizing was performed using the GeneMapper® and analyzed in Cervus, GenePop and Popgene softwares.

Mean number of alleles was observed as 6.643±2.061 with the range of three (MAF209 and SRCRSP3) to nine (OarFCB20 and OarAE54) with 93 total alleles. The mean expected heterozygosity, observed heterozygosity and Nei's heterozygosity values were 0.675±0.137, 0.553±0.194 and 0.665±0.135 respectively, indicating high genetic diversity among the studied loci. Estimated values of polymorphic information content and Shannon index showed that the most of the loci in this study were highly polymorphic and the values found to be 0.628±0.138 and 1.390±0.346 respectively. Deviations from Hardy-Weinberg equilibrium were observed for six of the studied loci. Ewens-Watterson neutrality test for microsatellite markers showed neutrality in all 14 markers, therefore no hitchhiking can be observed in any of the markers analyzed in this study. The mean of inbreeding coefficient within the population (Fis) by Weir and Cockerham method showed slightly higher value than Robertson and Hill method (0.183±0.223 and 0.163±0.212 respectively), suggesting that moderate level of inbreeding within Ardi population in Riyadh. Non-significant heterozygote excess was revealed from Sign test, standardized differences test and Wilcoxon tests, along with the normal 'L' shaped distribution of mode-shift test, indicated no bottleneck in recent past in Ardi goat. Therefore, any of unique
alleles present in this breed may not have been lost.

Results of this study suggest that primers used in this study are suitable for genetic characterization and linkage mapping projects. This breed still has good amount of genetic diversity. Moreover, traditional management system might be a possible reason for moderate level of inbreeding showed in Ardi goat. The conservation strategies of this local breed should be considered in near future. These results can be used to establish national conservation and breed improvement strategies for economic traits.