1. Comparative genomics of swine leukocyte antigen class I of Nigerian and Kenyan pigs
- Author
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E. Okoth, G. O. Omitogun, D. Bayene, O. O. Oluwole, and P. Roger
- Subjects
Immunoglobulin gene ,Genetics ,Comparative genomics ,Phylogenetic tree ,law ,GenBank ,Biology ,Domestication ,Mega ,Gene ,Polymerase chain reaction ,law.invention - Abstract
The classical genes are a member of immunoglobulin gene family that is involved in the presentation of antigen peptides. They are located in every nucleated cell surface, except in neurons and trophoblasts. They are synthesized in infected cell (viral infection), binding to viral proteins and giving rise to Swine Leucocyte Antigen (SLA) I- antigen complex. In the study, the SLA class I gene of Nigerian pigs with pigs from Kenya along with archived sequences from Asia and American pigs available on Genbank to gain a better understanding of matrilineal origin of Nigerian and Kenyan pigs. Gain insight into demographic distribution, their domestication and adaptation were compared. The deoxyribonucleic acid (DNA) was extracted from 90 pigs (60 Nigerian pigs (NP) and 30 pigs from Kenya) using Invitrogen Kit, quantified by using Nanodrop, and amplified by using Polymerase Chain Reaction. The expected bands were purified and sequenced for SLA class I. The sequences were aligned and phylogenetic tree was analyzed by using MEGA 6. BLAST (Basic Local Alignment Search Tools) was conducted in NCBI (National Center for Biotechnology Information). The sequences of Nigerian pigs and Kenya pigs were compared with published pig data in GenBank. Neighboring Joint (NJ) tree constructed with sequences from Nigeria, Kenya and other pigs from GenBank revealed that some of the NP clustered together with Asian pigs at the middle of the tree while some clustered just above the Kenyan below the tree and the outgroup homosapien stood out. The result from the calculation of total number of segregating sites gave the negative Tajima's D value (-0.181) while the non-significant difference (p > 0.05) obtained from the result showed that the null hypothesis was not rejected. In conclusion, there is genetic difference between the Nigerian and Kenyan pigs based on the phylogeny tree constructed. There is an excess of low frequency polymorphisms relative to population size. This may be as a result of evolutionary forces during course of adaptation in tropical countries in Africa. more...
- Published
- 2020
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