Thesis (Ph.D.) - Cairo University - Faculty of Agriculture - Department of Animal Production

This study aimed at genotyping the native and exotic rabbit breeds in Egypt and determining DNA barcodes of them. Rabbits of seven breeds were used in this experiment. The native breeds were Black Baladi (BB), White Baladi (WB), Red Baladi (RB) and Egyptian Jabali (JAB). The exotic breeds were New Zealand White (NZW), American Rex (AR) and Chinchilla (CH). Genotyping included detecting the microsatellite markers in 14 loci and sequencing the mitochondrial DNA (mtDNA) cytochrome oxidase 1 (CO1). The results revealed breeds varied in the observed number of alleles (No) and the effective number of alleles (Ne). The differences between No and Ne were small in WB (0.2), RB (0.2), AR (0.1) and CH (0.2), and this was possibly due to maintaining the breeds in small size populations. The differences were larger in the breeds BB (2.3), JAB (1.1) and NZW (2.0) and indicated possible inbreeding and/or selection. The observed heterozygosity (Ho) was intermediate to high among the breeds. The average expected heterozygosity (He) was the highest (0.82) in NZW and was the lowest (0.46 and 0.47) in AR and CH. The difference between Ho and He was small (0.01-0.06) in BB, WB, RB, JAB and NZW, and was large in AR (0.26) and CH (0.14). The mean polymorphic information content (PIC) was high in BB, JAB and NZW (PIC {u2265}0.50) and was moderate in WB, RB, AR and CH (PIC {u2264} 0.50). The FIS was negative in most of the loci and indicated the excess in heterozygosity and the decrease in homozygosity. Except JAB, there was overlapping between many breeds indicating possible gene exchange. The results of sequencing mtDNA revealed that the (A+G)/(C+T) ratio was different between breeds and ranged from 0.695 in BB to 0.714 in CH.The nucleotide diversity among breeds resulted in different gene encoding

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