Comparative analysis of sequence diversity diagram for five rabbit' breeds in Egypt using single nucleotide polymorphism

Abstract EN

The genes coded and referred to as 18S rDNA has been selected as a universal marker.

Sequence data from 18S rDNA was used to estimate the genetic variants on 128 rabbits belonging to five different breeds in Egypt, New Zealand White (NZW, n = 35), California (Ca, n = 35), Chinchilla (C, n = 19), Flander (F, n = 19) and Babion (B, n = 20).

Blood samples for sequencing were collected and sequence diversity diagram for multiple sequence alignments was performed.

In addition, the comparative analysis according to detected SNPs was implemented.

The results revealed that a 1115 bp fragment of DNA sequence was constructed using ABI5100 automated sequencer.

Random small DNA sequence mismatches (74 nucleotides ; 1-29, 1071-1115) has been detected.

The similarity between Ca and NZW breeds was 92 %, additionally, higher similarity percentage was observed between C and both of B, and F (97.02, 97.5 respectively).

Nine SNPs were detected; five single nucleotide polymorphisms w e re s p re a d t o (SNP : A > T, and T > A) for B and F located at 185, and 508 bp, also C > A and G > C for C located at 268, and 919 bp.

In addition, A > T for B located at 267 bp, and four SNPs between Ca and NZW located at 880, 886, 899, and 900 bp were detected.

The Maximum Likelihood was used to estimate the Transition/Transversion (ti / tv) Bias resulted in the estimated (ti / tv) bias (R) was 0.67.

Substitution pattern and rates were estimated, the nucleotide frequencies were A = 22.12%, T / U = 21.13 %, C = 26.72 %, and G = 29.99 %.

In conclusion, the utilized five rabbit breeds possess a good reservoir for diversity which is essential for genetic improvement.

Formal conservation plan is needed and must be implemented in Egypt to achieve such proper genetic improvement.