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Genetic Diversity in Exon 2 of the Major Histocompatibility Complex Class II DQB1 Locus in Nigerian Goats

Abstract

The DQB1 locus is located in the major histocompatibility complex (MHC) class II region and involved in immune response. We identified 20 polymorphic sites in a 228 bp fragment of exon 2, one of the most critical regions of the MHC DQB1 gene, in 60 Nigerian goats. Four sites are located in the peptide binding region, and 10 amino acid substitutions are peculiar to Nigerian goats, compared with published sequences. A significantly higher ratio of nonsynonymous/synonymous substitutions (d N/d S) suggests that allelic sequence evolution is driven by balancing selection (P < 0.01). In silico functional analysis using PANTHER predicted that substitution P56R, with a subPSEC score of −4.00629 (Pdeleterious = 0.73229), is harmful to protein function. The phylogenetic tree from consensus sequences placed the two northern breeds closer to each other than either was to the southern goats. This first report of sequence diversity at the DQB1 locus for any African goat breed may be useful in the search for disease-resistant genotypes.

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Acknowledgments

The authors are grateful to the College of Agriculture and Life Sciences and Mario Einaudi Center for International Studies of Cornell University, Ithaca, New York, for financial support. Many thanks to the Nigerian Government Tertiary Educational Trust Fund fellowship awarded through Nasarawa State University to AY. Approval of research visits by AY, MIT, MAA, and BOA to Cornell University by Prof. W. Ron Butler is gratefully acknowledged.

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Correspondence to Ikhide G. Imumorin.

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Yakubu, A., Salako, A.E., De Donato, M. et al. Genetic Diversity in Exon 2 of the Major Histocompatibility Complex Class II DQB1 Locus in Nigerian Goats. Biochem Genet 51, 954–966 (2013). https://doi.org/10.1007/s10528-013-9620-y

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Keywords

  • Genetic diversity
  • Exon 2
  • DQB1 gene
  • MHC class II
  • Nigerian goats
  • SNPs