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Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats

Abstract

Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats. Fourteen different types of alleles identified in the Nigerian goats, four of which were found in the peptide coding region (A57G, Q89R, G104D, and T112I), indicate a high degree of polymorphism at the DRB locus in this species. An obvious excess (P < 0.01) of non-synonymous substitutions than synonymous (dN/dS) in this locus is a reflection of adaptive evolution and positive selection. The phylogenetic trees revealed largely species-wise clustering in DRB gene. BsaHI, AluI, HaeIII, and SacII genotype frequencies were in Hardy-Weinberg equilibrium (P > 0.05), except AluI in RS goats and HaeIII in WAD goats (P < 0.05). The expected heterozygosity (H), which is a measure of gene diversity in the goat populations, ranged from 0.16 to 0.50. Genotypes AA (BsaHI), GG, GC and CC (AluI) and GG, GA, AA (HaeIII) appeared better in terms of heat tolerance. The heat-tolerant ability of SH and RS goats to the hot and humid tropical environment of Nigeria seemed better than that of the WAD goats. Sex effect (P < 0.05) was mainly on pulse rate and heat stress index, while there were varying interaction effects on heat tolerance. Variation at the DRB locus may prove to be important in possible selection and breeding for genetic resistance to heat stress in the tropics.

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Acknowledgements

Funding for this project was provided by the College of Agriculture & Life Sciences and Mario Einaudi Center for International Studies of Cornell University, Ithaca, NY through National Research Initiative Competitive Grant Program (Grant No. 2006-35205-16864) from the USDA National Institute of Food and Agriculture and is gratefully acknowledged. The research visit of A.Y. (ETF/DOPS/AST&D/UNIV/KEFFI/VOL.2) and M.I.T. to Cornell was made possible through the fellowships from the Nigerian Government Educational Trust Fund (ETF) now known as Tertiary Educational Trust Fund (TETFUND).

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Yakubu, A., Salako, A.E., De Donato, M. et al. Association of SNP variants of MHC Class II DRB gene with thermo-physiological traits in tropical goats. Trop Anim Health Prod 49, 323–336 (2017). https://doi.org/10.1007/s11250-016-1196-1

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Keywords

  • DRB locus
  • Single-nucleotide polymorphism
  • Genetic diversity
  • Heat tolerance
  • Goats