Trop Anim Health Prod (2017) 49:323–336
DOI 10.1007/s11250-016-1196-1
REGULAR ARTICLES
Association of SNP variants of MHC Class II DRB gene
with thermo-physiological traits in tropical goats
Abdulmojeed Yakubu 1,2,3 & Adebowale E. Salako 3 & Marcos De Donato 1,4 &
Sunday O. Peters 5 & Michael I. Takeet 1,6 & Mathew Wheto 7 & Moses Okpeku 8,9 &
Ikhide G. Imumorin 1
Received: 25 May 2016 / Accepted: 24 November 2016 / Published online: 1 December 2016
# Springer Science+Business Media Dordrecht 2016
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 sub-
stitutions 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
* Abdulmojeed Yakubu
abdul_mojeedy@yahoo.com
* Ikhide G. Imumorin
igi2@cornell.edu
1
Animal Genetics and Genomics Laboratory, International Programs,
College of Agriculture and Life Sciences, Cornell University,
Ithaca, NY 14853, USA
2
Department of Animal Science, Nasarawa State University,
Lafia, Nigeria
3
Department of Animal Science, University of Ibadan,
Ibadan, Nigeria
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
and HaeIII in WAD goats (P < 0.05). The expected heterozygos-
ity (H), which is a measure of gene diversity in the goat popula-
tions, 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.
Keywords DRB locus . Single-nucleotide polymorphism .
Genetic diversity . Heat tolerance . Goats
Introduction
Genetic studies of livestock populations focus on questions of
domestication, within- and among-breed diversity, breed history,
4
Laboratorio Genetica Molecular, IBB, Universidad de Oriente,
Cumana, Venezuela
5
Department of Animal Science, Berry College, Mt Berry, GA 30249,
USA
6
Department of Veterinary Microbiology and Parasitology, Federal
University of Agriculture, Abeokuta, Nigeria
7
Department of Animal Breeding and Genetics, University of
Agriculture, Abeokuta, Nigeria
8
Department of Livestock Production, Niger Delta University,
Amassoma, Nigeria
9
State Key Laboratory of Genetic Resources and Evolution, Chinese
Academy of Science (CAS), Kunming Institute of Zoology,
Kunming, Yunnan Province, China
324
and adaptive variation (Lenstra et al. 2012). Potential conserva-
tion issues in domestic animals have already been spotted by the
Food and Agriculture Organization of the United Nations (FAO)
with the objective of long-term conservation of genetic re-
sources for future use. Such a goal can be achieved by preserv-
ing the widest possible spectrum of genetic diversity because
future needs are unpredictable (FAO 2012). The detection of loci
affecting economically important traits represents a major objec-
tive of livestock genetics and genomics. It should ultimately lead
to more efficient breeding schemes and improve the accuracy
and intensity of selection programs.
Increasing attention has been put into understanding what
proportion of a genome or which genes are being shaped by
selection (Pariset et al. 2009). Directional (Darwinian) selection
can leave a set of signatures in the genes under its influence,
such as the rapid divergence of functional sites among species
and the depression of polymorphism within species. On the
basis of these signatures, it is possible to identify genes or
chromosomal regions which are likely targets of positive selec-
tion. The several complete-genome projects have led to the
emergence of single-nucleotide polymorphisms (SNP) as the
most modern genetic markers. SNP occur frequently in the
mammalian genome and are useful for rapid, large-scale, and
cost-effective genotyping for ecological and conservation stud-
ies and for population and evolutionary studies (Vignal et al.
2002; Cappuccio et al. 2006; Taberlet et al. 2011). These poly-
morphisms can be also be used as resources of markers for
association studies of complex diseases and for assessment of
individual predisposition to diseases (Carrington et al. 1999; Fan
et al., 2005). The identification of specific genes and gene path-
ways associated with complex infectious diseases can contribute
new knowledge for marker-assisted selection studies aimed at
increasing disease resistance in ruminants (Pisoni et al. 2010).
The major histocompatibility complex (MHC) is funda-
mental to the vertebrate immune system, encoding molecules
that bind parasite-derived peptides for presentation to T cells
and subsequent initiation of an immune response (Oliver and
Piertney 2012; Brinkmeyer-Langford et al. 2012). MHC loci
generally display considerably greater levels of nucleotide di-
versity and heterozygosity than the genomic average
(Gaudieri et al. 2000; De et al. 2003; Yakubu et al. 2013),
which is maintained by balancing selection acting through
antagonistic coevolution with parasites and/or mate choice
for MHC dissimilarity (Spurgin and Richardson 2010). The
MHC plays an important role in an organism’s ability to re-
spond to pathogens. Immunogenetic diversity is advantageous
as it permits the recognition of more external antigens. For this
reason, MHC and immune gene variation are considered a
barometer for the genetic health of animal populations.
MHC genes have been extensively studied as candidate genes
for disease resistance in many domestic animal species. The
DR genes are the best characterized. DRB is the most poly-
morphic class II gene, with 58 sequenced alleles and 6 DR
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Trop Anim Health Prod (2017) 49:323–336
variants detected by isoelectric focusing. The second exon of
the DRB gene, in particular, has been the most widely studied
region because it encodes peptide binding sites that are ex-
tremely polymorphic (Dongxiao and Yuan 2004; Doxiadis
et al. 2012). DRB genes encode proteins that play an impor-
tant role in the immune response, and their expressional reg-
ulation is crucial to the immune reaction. Sequence variation
at the regulatory region can directly affect the gene expression
level (Thomas et al. 2003; Fan et al. 2005). The genomic
variation at critical restriction sites may potentially be respon-
sible for susceptibility or resistance to certain diseases, and
this information may be of great concern to conserve any
species that is being counted endangered due to higher disease
susceptibility (Froeschke and Sommer 2012). The applicabil-
ity of DRB alleles as markers to detect vertebrate hybridiza-
tion has recently been documented (Alasaad et al. 2012).
The goat (Capra hircus, L.) represents one of the most
important farm animal species. It is reared in all continents
with an estimated world population of about 900 million an-
imals, out of which 55.1 million are reared in Nigeria
(FAOSTAT 2011). Goats play socio-economic and cultural
roles especially in the lives of rural dwellers and are found
in every zone, both in tsetse-free and tsetse-endemic areas of
the country. Despite its importance, studies on the goat ge-
nome are still in their infancy compared to those in other farm
animal species (Fontanesi et al. 2010).
Although the three major breeds of goats in Nigeria, name-
ly, West African Dwarf (WAD), Red Sokoto (RS), and Sahel
goats, have been characterized phenotypically (Yakubu et al.
2011), there is no information on genetic characterization in-
volving DRB gene. Therefore, the objective of this study was
to investigate molecular genetic variation and phylogenetic
diversity of DRB gene in Nigerian goat breeds and the asso-
ciation of their SNPs with thermo-physiological indices.
Materials and methods
Animals and blood collection
Blood samples were obtained from a total of 220 animals
(about 2 years of age) comprising 80 West African Dwarf
(WAD), 90 Red Sokoto (RS), and 50 Sahel (SH) goats of both
sexes sampled across various farms in Nigeria (Fig. 1). All the
animals were subjected to similar grazing patterns. Genomic
DNA from collected blood samples was isolated using the
ZymoBeadTM Genomic DNA kit (Zymo Research Corp.,
Irvine, CA, USA). The ethical guidelines of the International
Council for Laboratory Animal Science and Cornell
University, Ithaca, NY, USA were strictly followed. The quan-
tification of the DNA yield as well as the assessment of its
quality was done using Nanodrop ND-100 UV/Vis
Spectrophotometer (Nanodrop Technologies, Inc., DE, USA).
Trop Anim Health Prod (2017) 49:323–336
Fig. 1 Map of Nigeria showing
sampling locations
PCR amplification and sequencing of caprine MHC DRB
gene
A 284-bp fragment of exon 2 of DRB was amplified in seven
animals for polymorphism identification. Primers designed
were identical to those described by Amills et al. (1995).
P r i m e r s e q u e n c e s w e r e D R B 1 . 1 / F W, 5 ′ - TAT C
CCGTCTCTGCAGCACATTTC-3′ and DRB 1.2/REV, 5′-
TCGCCGCTGCACACTGAAACTCTC-3′. PCR amplifica-
tions were carried out in a C1000TM Thermal Cycler (Bio-
Rad, USA) with a total reaction volume of 20 μL containing
20–30 ng DNA, 10 pmol of each primer in 10 μL Syd Lab
PCR Premix (Syd Labs, Inc., Malden, USA) containing Taq
DNA polymerase, dNTPs, MgCl2, reaction buffer, PCR stabi-
lizer, and enhancer at optimal concentrations. The thermal
profile for amplifying the DRB exon 2 involved 30 cycles of
initial denaturation at 94 °C for 5 min, denaturation at 94 °C
for 60 s, annealing at 60 °C for 90 s, extension at 72 °C for
90 s, and elongation at 72 ° for 10 min. PCR products were
detected on 1.0% agarose gel including 0.5 μg/mL of GelRed
nucleic acid stain and scored using GENEMate Quanti-
Marker 100 bp DNA ladder (BioExpress, UT, USA). The
PCR products were visualized after the gel electrophoresis
using an ultraviolet transilluminator (SpectrolineR TC 312 E)
and photographed under UV light (Alpha imager).
Sequencing of the amplified fragments was carried out using
the same PCR primer with the Applied Biosystems
Automated 3730XL DNA Analyzer using Big Dye
Terminator chemistry and AmpliTaq-FS DNA Polymerase.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
325
SNP identification and restriction fragment length
polymorphism (RFLP) analysis
Single-nucleotide polymorphisms (SNPs) were identified in
DRB gene with the aid of CodonCode Aligner software and
MEGA version 5 (Tamura et al. 2011). In the RFLP analysis,
20 μL of concentrated PCR products was digested for 4 h at
37 °C with BsaHI (tag no. R0556s), AluI (tag no. R0137s),
HaeIII (tag no. R0108T), and SacII (tag no. R0157s) (New
England Biolabs, USA) according to the manufacturers’ in-
structions. The restriction fragments were resolved by 1.0%
agarose gel electrophoresis and were visualized using an ul-
traviolet transilluminator (SpectrolineR TC 312 E). The pre-
dicted fragments for BsaHI (allele 1 = 174, 112 and allele
2 = 284), AluI (allele 1 = 158, 42, 84 and allele 2 = 200, 84),
HaeIII (allele 1 = 153, 14, 117 and allele 2 = 167, 117) and
SacII (allele 1 = 223, 63 and allele 2 = 284) were involved.
Physiological data collection and analysis
Rectal temperature (RT, °C), skin temperature (ST, °C), respi-
ratory rate (RR, breaths per minute), and pulse rate (PR, beats
per minute) were measured early in the morning between 7:00
A.M. and 8:00 A.M. before sunrise. Repeated measurements for
RT, ST, RR, and PR were carried out between 4:00 P.M. and
5:00 P.M. Thermo-physiological measurements were taken on
adult animals in the months of November, February, and
March corresponding to the period of peak environmental tem-
peratures in Nigeria. Sampling was done in such a way that
326
each breed and sex was adequately represented in each month.
Unhealthy and pregnant animals were not sampled as these
may influence thermo-physiological parameters.
RT was taken on each animal using a digital thermometer.
The sensory tip was disinfected and inserted into the rectum at
the display of L°C by a thermometer (which indicated that the
thermometer is set for temperature reading). This was re-
moved after the sound of the alarm signal. The displayed body
temperature was then recorded. RR was determined by
counting the number of flank movements per minute. PR
was measured by placing the fingertips on the femoral arteries
of the hind limb for 1 min. The relationship between the mea-
sured RR and PR together with their normal average values
was used to derive heat stress index (HSI) according to the
method of Oladimeji et al. (1996):
HSI ¼ ðRR=PRÞ  ðNPR=NRRÞ
where
RR measured respiratory rate
PR measured pulse rate
NPR normal pulse rate
NRR normal respiratory rate.
Sequence and phylogenetic analysis
Sequence alignments, translations, and comparisons were car-
ried out using ClustalW (Larkin et al. 2007). The BLAST al-
gorithm was used to search the NCBI GenBank (http://www.
ncbi. nlm.nih.gov/) databases for homologous sequences. We
performed a compilation of a representative number of
Nigerian goat DRB sequences (7 in number) identified in the
present study and published goat (17), sheep (11), cattle [Bos
taurus (5) and Bos indicus (5)], buffalo (5), and porcine (1) (as
an outgroup) DRB sequences from GenBank following the
method of De et al. (2011). The GenBank accession numbers
of these sequences were AB008345.1, AB008347.1,
AB008348.1, AB008349.1, AB008350.1, AB008351.1,
AB008352.1, AB008353.1, AB008354.1, AB008355.1,
AB008356.1, AB008357.1, AB008358.1, AB008359.1,
AB008360.1, AB008361.1, and AB008362.1 (goat);
U00204.1, U00205.1, U00206.1, U00207.1, U00208.1,
U00209.1, AF126433.1, AF126434.1, AF126435.1,
AF126436.1, and AY884014.2 (sheep); FJ381736.1,
FJ381738.1, FJ381739.1, FJ381751.1, and AY847739.1 (Bos
taurus); AF272872.1, AF272873.1, AF272879.1,
DQ834894.1, and DQ834902.1 (Bos indicus); AF270664.1,
AF270665.2, AF270666.1, AF270667.1, and AF270668.1
(buffalo); and AY365420.1 (swine), respectively.
The deduced DRB amino acid sequences of Nigerian goats
were compared with published caprine amino acid sequences.
The Capra hircus DRB-AB008345.1 complete coding
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Trop Anim Health Prod (2017) 49:323–336
sequence (CDS) (Takada et al. 1998) was used as the reference
sequence. The relative proportions of non-synonymous sub-
stitutions per non-synonymous site (dN) and the number of
synonymous substitutions per synonymous site (dS) were cal-
culated for Nigerian goats using the method of Tamura Nei to
test for evidence of positive selection at the DRB locus. The
ratio of non-synonymous to synonymous divergence (dN/dS)
in Nigerian goats was tested for departure from the neutral
expectation of unity using the codon-based Z-distribution as
by modified Nei-Gojobori, applying Jukes-Cantor correction.
A neighbor-joining tree on the basis of genetic distances,
depicting phylogenetic relationships among Nigerian goat
DRB nucleotide sequences and published goat, sheep, Bos
taurus, Bos indicus, buffalo, and porcine (outgroup) sequences,
was constructed using the complete deletion and Kimura-2 pa-
rameter model options. The reliability of the tree was estimated
by bootstrap confidence values, with 1000 bootstrap replica-
tions. The rate variation among sites was modeled with a gam-
ma distribution (shape parameter = 0.5). All the DRB sequences
were trimmed to a similar length (234 bp) corresponding to the
same region of exon 2 before generating the trees. MEGA ver-
sion 5 (Tamura et al. 2011) was employed in the analysis.
Statistical analysis
Genotype and allele frequencies of BsaHI, AluI, HaeIII, and
SacII were determined by direct counting as described by
Falconer and Mackay (1996). Allele and genotype frequencies
of each gene in each goat population were tested for Hardy-
Weinberg equilibrium (HWE), and the differences between the
observed and expected numbers of each allele and genotype
were compared using a goodness-of-fit chi-square (χ2) test.
HWE was assumed for P >0.05 using POPGENE Statistical
Software (Yeh et al. 1999). Heterozygosity (He) was estimated
as the expected proportion of heterozygotes under HWE. Data
were also analyzed using the general linear model (GLM) of
SAS (2010) statistical software to test the fixed effects of SNP
genotype, breed, and sex as well as their interactions on phys-
iological indices (RT, ST, RR, PR, and HSI). Means were sep-
arated using Duncan’s multiple range test (DMRT) at 95% con-
fidence interval. The following linear model was employed:
Yijk μ + Gi + Bj + Sk + (GB)ij + (GS)ik + (BS)jk +
(GBS)ijk + eijkl
Yijk individual observation
μ overall mean
Gi fixed effect of ith SNP genotype [i = GG, GA, AA
(BsaHI), GG, GC, CC (AluI), GG, GA, CC
(HaeIII), AA, AC, CC (SacII)].
Bj fixed effect of jth breed (j = WAD, RS, SH)
Sk fixed effect of kth sex (k = male, female)
(GB)ij interaction effect of ith SNP genotype and jth breed
(GS)ik interaction effect of ith SNP genotype and kth sex
Trop Anim Health Prod (2017) 49:323–336 327

polymorphism at the DRB locus in this species. Out of these,

Fig. 2 A 284-fragment size of DRB gene in Nigerian goats
(BS)jk interaction effect of jth breed and kth sex
(GBS)ijk interaction effect of SNP genotype, breed, and sex
eijkl random error associated with each record
(normally, independently, and identically
distributed with zero mean and constant variance)
Results
Amplification by PCR of the DBR gene of Nigerian goats
produced a 284-fragment size (Fig. 2).
Alignment of deduced amino acid sequences of the DRB
exon 2 of Nigerian goat alleles and the published caprine se-
quences are shown in Fig. 3. Fourteen different types of alleles
identified in the Nigerian goats indicate a high degree of
four (A57G, Q89R, G104D, and T112I) were found in the
peptide coding region while ten were located outside the pep-
tide binding region. However, the amino acid substitution,
R54W, was peculiar to the Nigerian goats when compared with
the published caprine sequences. Codon-based Z test using the
Nei-Gojobori method revealed that at 5% level of significant
difference from unity, dN was greater than dS indicating posi-
tive selection at the DRB locus of Nigerian goats (dS = 0.280
± 0.08, dN = 0.48 ± 0.09, dN/dS = 1.71; Z-statistic = 2.05).
Figure 4 shows the neighbor-joining tree for the seven
Nigerian goat DRB nucleotide sequences and the published
caprine, bovine, buffaline, and porcine (outgroup) sequences.
The phylogenetic analysis revealed that the Nigerian goats
DRB sequences were more related to the published caprine
DRB sequences. A similar pattern of clustering was observed
for the ovine, bovine, and buffaline sequences. Species-wise,
the goat sequences seemed more related to the ovine com-
pared to the bovine and buffaline sequences at this locus.
However, the inter-generic distances in general were more
than the intra-generic distances.
Using the published Capra nucleotide sequence with acces-
sion number AB008345 as the referenced sequence, BsaHI
(G256A) caused a change from GAC (aspartic acid) to AAC
(asparagine); AluI (G285C) caused a change from GAG
(glutamic acid) to GAC (aspartic acid); HaeIII (G238A), a
change from GCC (alanine) to ACC (threonine); and SacII
(A308C), a change from GAG (glutamic acid) to GCG (alanine).
Three genotypes (GG, GA, and AA), (GG, GC, and CC), (GG,
GA and AA), and (AA, AC and CC) were observed in BsaHI,
AluI, HaeIII, and SacII RFLP of DRB gene in Nigerian goats
(Table 1). The respective two alleles were (G and A), (G and C),

Fig. 3 Comparison between the * * * *

predicted amino acid sequences #Goat-AB008345.1 FGTGRVRAQI LLVRDSLGRP GGRGGQVLEQ PEGPGAGGGH GQTLRGEFHC
of Nigerian goats MHC DRB #Goat-AB008347.1 ...E...G.. .I...N.... ....A..... .........Q V.I.......
exon 2 alleles, and the #Goat-AB008348.1 ...E...G.. .I...N.... ....A..... .........Q V.I.......
corresponding previously #Goat-AB008349.1 ...E...G.. .I...N.... ....A..... .....P.R.. V.........
reported caprine sequences. #Goat-AB008350.1 ...E...G.. .I...N.... ....A..... .....P.R.. V.........
Identity is denoted by dots (.). An #Goat-AB008351.1 ...E...G.. .I........ ....A..... ......D... V.........
asterisk indicates a peptide #Goat-AB008352.1 ...E...G.. .I........ ....A..... ......D... V.......Q.
binding site following the #Goat-AB008353.1 ...E...G.. .I........ ....A..... .......R.. V.......Q.
#Goat-AB008354.1 ...E...G.. .I........ ....A..... .....P.R.. V.........
description of Naskar et al. (2012)
#Goat-AB008355.1 ...E...G.. .I...N.... .S..A..... ......D... V.........
#Goat-AB008356.1 ...E...G.. .I....P... ....AR.... .......... ..........
#Goat-AB008357.1 ...E...G.. .I........ ....AR.... ...S..D... ..........
#Goat-AB008358.1 ...E...G.. .I........ ....A..... ...S..D... V.........
#Goat-AB008359.1 ...E...G.V .IL....... ....AR.... .K....D... V.........
#Goat-AB008360.1 .......... .......... .......... .......... ..........
#Goat-AB008361.1 .......... ..L....... .....R.... .......... ..........
#Goat-AB008362.1 ...E..GG.. .I........ .S..AR.... .....ED... V.........
#Nigerian-goat1 ...E...G.. .I...N.... .S..A..... ......D... V.......Q.
#Nigerian-goat2 ...E...G.. .I...N.... .S..A..... ......D... V.......Q.
#Nigerian-goat3 ...E...G.. .I........ ....A..... ......D... V.......Q.
#Nigerian-goat4 .......... .......... .......... .......... ........Q.
#Nigerian-goat5 ...E..WG.. .I...N.... ....A..... ......D... V.......Q.
#Nigerian-goat6 ...E...G.. .I...N.... .S..A..... ......D... V.......Q.
#Nigerian-goat7 ...E...G.. .IL....... .S..AR.... .....ED... V.I.....Q.

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328 Trop Anim Health Prod (2017) 49:323–336

Fig. 4 Phylogenetic tree derived from sequences of each of Nigerian goat breeds and those of published caprine, ovine, and bovine DRB alleles. The
evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length = 11.27576839 is shown

(G and A), and (A and C). In BsaHI, the GG, GA, and AA
genotype frequencies were 0.29, 0.45, and 0.26 (WAD); 0.32,
0.47, and 0.22 (RS); and 0.35, 0.54, and 0.10 (SH). The respec-
tive G and A gene frequencies were 0.51 and 0.49 (WAD), 0.55
and 0.45 (RS), and 0.63 and 0.37 (SH). For AluI, the GG, GC,
and CC genotype frequencies were 0.45, 0.45, and 0.10 (WAD);
0.18, 0.64, and 0.18 (RS); and 0.14, 0.45, and 0.41 (SH). The G
and C allele frequencies were 0.67 and 0.33 (WAD), 0.50 and
0.50 (RS), and 0.36 and 0.64 (SH), respectively. In HaeIII, the
GG, GA, and AA frequencies were 0.41, 0.36, and 0.23 (WAD);
0.26, 0.43, and 0.31 (RS); and 0.34, 0.46, and 0.20 (SH); while
the gene frequencies for G and A were 0.59 and 0.41 (WAD),
0.47 and 0.53 (RS), and 0.57 and 0.43 (SH), respectively.
However, in SacII, the AA, AC, and CC values were 0.54,
0.39, and 0.07 (WAD); 0.82, 0.18, and 0.00 (RS); and 0.69,
0.29, and 0.02 (SH), respectively. The corresponding A and C
allele frequencies were 0.74 and 0.26 (WAD), 0.91 and 0.09
(RS), and 0.83 and 0.17 (SH), respectively.
With the exception of RS goats in AluI and WAD goats in
HaeIII (P < 0.05 in both cases), the χ2 analysis showed no
significant differences (χ2 = 3.841; P > 0.05) in the observed
and the expected frequencies of the three genotypes in BsaHI,
AluI, HaeIII and SacII RFLP of DRB gene in the three Nigerian
goat breeds. While the non-significant χ2 values were consis-
tent with Hardy-Weinberg equilibrium (HWE), the significant
χ2 values violated the theoretical proportions. The heterozygos-
ity (gene diversity index) in BsaHI were 0.50, 0.50, and 0.47 for
WAD, RS, and SH goats, respectively. As regards AluI, the

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Trop Anim Health Prod (2017) 49:323–336 329

Table 1 Distribution of BsaHI,

AluI, HaeIII, and SacII (DRB) Breed Male Female Total Genotype frequency Gene χ2 H
genotypes and gene frequencies frequency
in Nigerian goats
BsaHI GG GA AA G A

WAD 25 52 77 22 (0.29) 35 (0.45) 20 (0.26) 0.51 0.49 0.63ns 0.50

RS 24 64 88 28 (0.32) 41 (0.47) 19 (0.22) 0.55 0.45 0.30ns 0.50
SH 26 22 48 17 (0.35) 26 (0.54) 5 (0.10) 0.63 0.37 1.14ns 0.47
AluI GG GC CC G C
WAD 20 38 58 26 (0.45) 26 (0.45) 6 (0.10) 0.67 0.33 0.02ns 0.44
RS 18 49 67 12 (0.18) 43 (0.64) 12(0.18) 0.50 0.50 5.39* 0.50
SH 16 13 29 4 (0.14) 13 (0.45) 12 (0.41) 0.36 0.64 0.03ns 0.46
HaeIII GG GA AA G A
WAD 26 54 80 33 (0.41) 29 (0.36) 18 (0.23) 0.59 0.41 4.92* 0.48
RS 25 65 90 23 (0.26) 39 (0.43) 28 (0.31) 0.47 0.53 1.65ns 0.50
SH 26 24 50 17 (0.34) 23 (0.46) 10 (0.20) 0.57 0.43 0.20ns 0.49
SacII AA AC CC A C
WAD 20 37 57 31 (0.54) 22 (0.39) 4 (0.07) 0.74 0.26 0.01 ns 0.38
RS 16 46 62 51 (0.82) 11 (0.18) 0 (0.00) 0.91 0.09 0.57 ns 0.16
SH 26 22 48 33 (0.69) 14 (0.29) 1 (0.02) 0.83 0.17 0.12 ns 0.28

Chi-square (χ2 ) (P < 0.05) = 3.841; *significant at P < 0.05; ns not significant (P > 0.05)
H heterozygosity (gene diversity index)

values for WAD, RS, and SH goats were 0.44, 0.50, and 0.46,
respectively. In HaeIII, 0.48, 0.50, and 0.49 values were record-
ed for WAD, RS, and SH goats, respectively. However, the
values recorded for WAD, RS, and SH goats in SacII were
0.38, 0.16, and 0.28, respectively.
The effects of DRB SNP genotypes on heat-tolerant traits
of Nigerian goat breeds are presented in Table 2. Under
BsaHI, genotype AA had a comparative advantage in skin
temperature [38.56 ± 0.17 (GG), 38.56 ± 0.12 (GA), and
37.52 ± 0.23 (AA); P < 0.05] and rectal temperature [39.16
± 0.12 (GG), 39.17 ± 0.09 (GA), and 38.41 ± 0.17 (AA);
P < 0.05]. Genotypes GG and CC in AluI appeared better in
terms of pulse rate [96.05 ± 5.25 (GG), 112.40 ± 3.68 (GC),
and 100.54 ± 5.13 (CC); P < 0.05] and respiratory rate [47.13
± 2.74 (GG), 46.59 ± 1.92 (GC), and 38.00 ± 2.68 (CC);
P < 0.05]. As regards the heat stress index, however, both

Table 2 Effect of DRB SNP

genotypes on heat tolerant traits SNP Pulse rate Respiratory rate Skin temperature Rectal temperature Heat stress index
of Nigerian goat breeds
BsaHI
GG 97.88 ± 4.54 45.31 ± 2.13 38.56 ± 0.17a 39.16 ± 0.12a 2.08 ± 0.11
GA 107.56 ± 3.29 47.20 ± 1.54 38.56 ± 0.12a 39.17 ± 0.09a 1.99 ± 0.08
AA 96.97 ± 6.10 41.08 ± 2.86 37.52 ± 0.23b 38.41 ± 0.17b 1.92 ± 0.15
AluI
GG 96.05 ± 5.25b 47.13 ± 2.74a 38.46 ± 0.21 39.15 ± 0.13 2.20 ± 0.14a
GC 112.40 ± 3.68a 46.59 ± 1.92a 38.68 ± 0.15 39.28 ± 0.09 1.87 ± 0.10ab
CC 100.54 ± 5.13ab 38.00 ± 2.68b 38.39 ± 0.21 39.25 ± 0.13 1.66 ± 0.14b
HaeIII
GG 84.50 ± 3.61c 52.62 ± 1.75a 38.52 ± 0.13 39.16 ± 0.09 2.62 ± 0.09a
GA 116.48 ± 3.18a 41.58 ± 1.54b 38.54 ± 0.11 39.16 ± 0.08 1.59 ± 0.08c
AA 101.01 ± 4.37b 46.72 ± 2.12b 38.71 ± 0.15 39.23 ± 0.10 2.05 ± 0.11b
SacII
AA 103.57 ± 2.97 48.01 ± 1.33 38.58 ± 0.10 39.23 ± 0.07 2.10 ± 0.08
AC 103.51 ± 4.72 45.90 ± 2.11 38.49 ± 0.16 39.23 ± 0.10 1.95 ± 0.12
CC 95.83 ± 13.73 40.67 ± 6.14 39.05 ± 0.48 39.23 ± 0.30 1.94 ± 0.35

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330 Trop Anim Health Prod (2017) 49:323–336

Table 3 Effect of breed on heat

tolerant traits of Nigerian goat Breed Pulse rate Respiratory rate Skin temperature Rectal temperature Heat stress index
breeds
BsaHI
WAD 83.20 ± 4.62b 54.79 ± 2.17a 38.70 ± 0.17a 39.20 ± 0.13a 2.78 ± 0.12a
RS 108.63 ± 3.87a 43.67 ± 1.81b 37.93 ± 0.15b 38.85 ± 0.11b 1.74 ± 0.10b
SH 110.58 ± 5.69a 35.13 ± 2.67c 38.01 ± 0.21b 38.68 ± 0.16b 1.48 ± 0.14b
AluI
WAD 85.09 ± 4.42b 53.21 ± 2.31a 38.83 ± 0.18a 39.34 ± 0.11 2.66 ± 0.12a
RS 115.61 ± 3.92a 43.84 ± 2.05b 38.19 ± 0.16b 39.27 ± 0.10 1.66 ± 0.11b
SH 108.29 ± 5.70aa 34.66 ± 2.97c 38.51 ± 0.23ab 39.08 ± 0.14 1.42 ± 0.16b
HaeIII
WAD 88.43 ± 3.53b 56.45 ± 1.71a 38.82 ± 0.12 39.08 ± 0.08 2.77 ± 0.09a
RS 105.22 ± 3.37a 47.62 ± 1.63b 38.43 ± 0.12 39.32 ± 0.08 2.01 ± 0.08b
SH 108.31 ± 4.29a 36.86 ± 2.08c 38.49 ± 0.15 39.00 ± 0.10 1.48 ± 0.10c
SacII
WAD 82.68 ± 5.63b 52.42 ± 2.52a 38.85 ± 0.10 39.18 ± 0.12 2.68 ± 0.14a
RS 113.90 ± 5.46a 47.00 ± 2.44a 38.34 ± 0.19 39.46 ± 0.12 1.78 ± 0.14b
SH 115.70 ± 6.93a 36.59 ± 3.10b 38.64 ± 0.24 39.11 ± 0.15 1.38 ± 0.18b

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genotypes CC and GC appeared to have superior advantage.
Under HaeIII, heat stress index appeared better off in geno-
type GA compared to others [2.62 ± 0.09 (GG), 1.59 ± 0.08
(GA), and 2.05 ± 0.11 (AA); P < 0.05]. The values for pulse
rate which were lower in genotypes GG and AA were 84.50 ±
3.61 (GG), 116.48 ± 3.18 (GA), and 101.01 ± 4.37 (AA)
(P < 0.05) while those for respiratory rate which appeared bet-
ter in genotypes GA and AA were 52.62 ± 1.75 (GG), 41.58 ±
1.54 (GA), and 46.72 ± 2.12 (AA) (P < 0.05). There were,
however, no SNP genotype effect (P > 0.05) on thermal indi-
ces under SacII.
Varying breed-dependent thermo-physiological responses
(P < 0.05) were observed in WAD, RS, and SH goats differ-
entially in the BsaHI, AluI, HaeIII, and SacII RFLP of DRB
gene (Table 3). The heat tolerance ability of SH and RS goats
to the hot and humid tropical environment of Nigeria seemed
better than that of the WAD goat.
Sex effect (P < 0.05) was mainly on pulse rate in the BsaHI,
AluI, HaeIII, and SacII RFLP of DRB gene, where male an-
imals seemed to have an advantage over the females (Table 4).
However, in SacII, heat stress index was significantly lower
(P < 0.05) in females than males.
The analysis of variance showed varying interaction effects
on the parameters measured (Table 5). Interaction effect of SNP
and breed (BsaHI) was significant (P < 0.01) on skin tempera-
ture and rectal temperature. Under AluI, interaction effect of
breed × sex as well as the three-way interaction of SNP ×
breed × sex was significant (P < 0.01) on pulse rate. In HaeIII,

Table 4 Effect of sex on heat tolerance traits of Nigerian goats

Sex Pulse rate Respiratory rate Skin temperature Rectal temperature Heat stress index

BsaHI
Male 91.36 ± 4.26b 43.24 ± 2.00 38.24 ± 0.16 38.92 ± 0.12 2.06 ± 0.11
Female 110.24 ± 3.51a 45.82 ± 1.64 37.18 ± 0.13 38.90 ± 0.10 1.94 ± 0.09
AluI
Male 93.00 ± 4.13b 43.12 ± 2.15 38.37 ± 0.17 39.16 ± 0.10 2.03 ± 0.11
Female 112.99 ± 3.60a 44.68 ± 1.88 38.65 ± 0.15 39.29 ± 0.09 1.79 ± 0.10
HaeIII
Male 94.31 ± 1.61b 45.95 ± 1.61 38.61 ± 0.12 39.20 ± 0.08 2.06 ± 0.11
Female 107.00 ± 2.79a 48.00 ± 1.35 38.55 ± 0.10 39.17 ± 0.07 1.94 ± 0.09
SacII
Male 92.47 ± 4.77b 46.87 ± 2.13 38.56 ± 0.17 39.30 ± 0.10 2.22 ± 0.12a
Female 110.30 ± 5.46a 44.67 ± 2.30 38.71 ± 0.18 39.17 ± 0.11 1.82 ± 0.13b

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Trop Anim Health Prod (2017) 49:323–336 331

Table 5 Analysis of variance

showing the interaction effects of Source of variation Mean squares and level of significance
DRB SNP genotype, breed, and
sex on heat tolerance traits of df PR RR ST RT HSI
Nigerian goats
BsaHI
SNP × breed 4 38.31ns 150.59ns 5.37** 3.39** 0.34ns
Residual 195 945.93 207.87 1.33 0.70 0.60
AluI
Breed × sex 2 4117.30** 43.94ns 0.06ns 0.29ns 0.46ns
SNP × breed × sex 4 2317.30** 1.82ns 1.54ns 0.49ns 1.12ns
Residual 136 645.67 175.81 1.04 0.41 0.49
HaeIII
SNP × breed 4 1756.51ns 195.78ns 1.29ns 0.24ns 1.36*
ns
Breed × sex 2 3635.92** 178.45 0.59ns 0.46ns 0.18ns
Residual 202 792.43 186.43 0.98 0.45 0.47

df degree of freedom, PR pulse rate, RR respiratory rate, ST skin temperature, RT rectal temperature, HSI heat
stress index
**Significant at P < 0.01; *significant at P < 0.05; ns non-significant

SNP × breed interaction effect was significant (P < 0.05) on
heat stress index while the breed and sex interaction effect
was on pulse rate (P < 0.01) (Tables 6, 7, 8, 9, and 10).
Discussion
The functional importance of MHC variability in parasite re-
sistance has defined the MHC as a paradigm for ecologically
important genetic variation and genetic health in natural pop-
ulations (Sommer, 2005). Comparison of predicted amino ac-
id residues of DRB exon 2 alleles with similar alleles from
other ruminants revealed considerable congruence in amino
acid substitution pattern. The extensive polymorphism ob-
served at the CLADRB locus in this study shows the charac-
teristics of MHC which include multiple nucleotide substitu-
tions between alleles, and a large number of alleles. The high
genetic diversity observed in livestock populations could also
be explained by overlapping generations, mixing of popula-
tions from different geographical locations, natural selection
favoring heterozygosis, or subdivision accompanied by genet-
ic drift. The peculiar R54W substitution in Nigerian goats may
be relevant in future studies to ascertain whether it is associ-
ated with productive, reproductive, and disease traits. The
non-synonymous/synonymous substitution rate ratio
(ω = dN/dS) has been widely used as a measure of selective
pressure on a gene. Whereas ratios larger than one indicate a
fitness advantage for mutations resulting in an amino acid
change (i.e., positive selection), ratios smaller than one sug-
gest selection against deleterious mutations (i.e., purifying se-
lection) (Kamath and Getz 2011). The higher dN value ob-
served in Nigerian goats might be due to the traditional breed-
ing practices. These practices, according to Das et al. (2012),
provide animals with adequate exposure to native environ-
mental conditions and natural mating pressures, thereby
playing an influential role in the development of optimal

Table 6 Interaction effect of SNP

and breed (BsaHI) on heat Breed SNP Parameters
tolerance traits of Nigerian goats
PR RR ST RT HSI

WAD GG 81.76 ± 9.55 56.79 ± 4.48 38.52 ± 0.36a 38.96 ± 0.26b 2.92 ± 0.24
GA 90.25 ± 5.20 58.26 ± 2.44 38.75 ± 0.20a 39.37 ± 0.14a 2.81 ± 0.13
AA 77.59 ± 8.60 49.31 ± 4.03 38.83 ± 0.32a 39.27 ± 0.23a 2.602 ± 0.22
RS GG 105.52 ± 6.07 41.71 ± 2.84 38.63 ± 0.23a 39.53 ± 0.17a 1.77 ± 0.15
GA 114.39 ± 5.80 48.37 ± 2.70 38.39 ± 0.22a 39.05 ± 0.16a 1.87 ± 0.15
AA 105.98 ± 8.01 40.91 ± 3.76 36.76 ± 0.30b 37.98 ± 0.22a 1.58 ± 0.20
SH GG 106.36 ± 7.58 37.43 ± 3.55 38.54 ± 0.28a 38.99 ± 0.21b 1.55 ± 0.19
GA 118.04 ± 6.03 34.96 ± 2.83 38.54 ± 0.23a 39.09 ± 0.16a 1.30 ± 0.15
AA 107.33 ± 14.04 33.00 ± 6.58 36.96 ± 0.53b 37.98 ± 0.38a 1.35 ± 0.35

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332 Trop Anim Health Prod (2017) 49:323–336

Table 7 Interaction effect of

breed and sex (AluI) on heat Sex Breed Parameters
tolerance traits of Nigerian goats
PR RR ST RT HSI

Male WAD 86.98 ± 7.21b 53.42 ± 3.76 38.71 ± 0.29 39.37 ± 0.18 2.64 ± 0.20
RS 107.604 ± 6.35a 43.65 ± 3.31 38.09 ± 0.26 39.22 ± 0.16 1.81 ± 0.17
SH 84.42 ± 7.81b 32.32 ± 4.08 38.32 ± 0.31 38.89 ± 0.20 1.63 ± 0.21
Female WAD 83.20 ± 5.14b 53.01 ± 2.68 38.96 ± 0.21 39.31 ± 0.13 2.69 ± 0.14
RS 123.62 ± 4.62a 44.03 ± 2.41 38.28 ± 0.19 39.31 ± 0.12 1.50 ± 0.13
SH 132.15 ± 8.29a 37.00 ± 4.33 38.70 ± 0.33 39.26 ± 0.21 1.20 ± 0.23

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genetic diversity, beneficial selection pressures, and adaptive
genetic diversity of DRB locus. This is buttressed by the
findings of McDonald and Kreitman (1991) that genes that
had a higher ratio of non-synonymous to synonymous substi-
tutions may have undergone adaptive evolution. As pathogens
are thought to be the main factor driving positive selection and
influencing polymorphism of the MHC loci, it has also been
speculated that the excess of non-synonymous substitutions
favored by positive selection was driven by the need for path-
ogen resistance (Li et al. 2012).
Cattle, sheep, and goat, in spite of their early domestica-
tion process, represented many DRB alleles with high het-
erozygosities and intermediate to large genetic distances
between them (Mikko et al. 1999; Nikbakht et al. 2012).
This indicated their higher adaptability supported by very
large effective population size spread over different geo-
graphical regions. Heterozygosity is considered advanta-
geous because individuals with two different alleles can
potentially present a wider range of pathogen-derived pep-
tides than can homozygotes. Data supporting heterozygote
advantage in the MHC are relatively scarce; an example is a
study of parasitism in naturally infected lambs (Stear et al.
2005). Therefore, the SNPs obtained in the present study
may have an enormous potential to be used as markers for
identifying the animals as susceptible or resistant to a par-
ticular disease(s). Besides the potential of DRB SNPs as a
candidate gene marker for various livestock diseases
(Amills et al. 1995), certain production (Sheikh et al.
2009) and reproduction traits (Renord and Vaiman 1989)
in livestock populations have been summarized.

Table 8 Interaction effect of

SNP, breed, and sex (AluI) on Sex SNP Breed Parameters
heat tolerance traits of Nigerian
goats PR RR ST RT HSI

Male GG WAD 94.70 ± 8.04a 58.00 ± 4.19 39.01 ± 0.32 38.99 ± 0.20 2.70 ± 0.22
RS 112.50 ± 12.71a 49.00 ± 6.63 38.25 ± 0.51 39.48 ± 0.32 2.15 ± 0.35
SH 75.00 ± 17.97a 38.00 ± 9.38 37.95 ± 0.72 39.00 ± 0.45 2.01 ± 0.49
GC WAD 74.25 ± 8.98b 58.25 ± 4.69 38.16 ± 0.36 39.48 ± 0.23 3.11 ± 0.25
RS 123.11 ± 8.47a 47.56 ± 4.42 38.88 ± 0.34 39.33 ± 0.21 1.56 ± 0.23
SH 95.50 ± 8.04b 31.70 ± 4.19 38.79 ± 0.32 39.13 ± 0.20 1.48 ± 0.22
CC WAD 92.00 ± 17.97a 44.00 ± 9.38 38.95 ± 0.72 39.65 ± 0.45 2.10 ± 0.49
RS 87.20 ± 11.36b 34.40 ± 5.93 37.14 ± 0.48 38.86 ± 0.29 1.72 ± 0.31
SH 82.75 ± 12.71b 27.25 ± 6.63 38.23 ± 0.51 38.55 ± 0.32 1.41 ± 0.35
Female GG WAD 68.88 ± 6.35b 52.75 ± 3.32 39.02 ± 0.26 39.24 ± 0.16 3.16 ± 0.17
a
RS 113.25 ± 8.98 45.00 ± 4.69 38.05 ± 0.36 39.08 ± 0.23 1.65 ± 0.25
SH 112.00 ± 17.97a 40.00 ± 9.38 38.45 ± 0.72 39.10 ± 0.45 1.52 ± 0.49
GC WAD 99.72 ± 5.99a 57.78 ± 3.13 38.86 ± 0.24 39.20 ± 0.15 2.47 ± 0.16
RS 120.47 ± 4.36a 48.24 ± 2.27 38.32 ± 0.18 39.14 ± 0.11 1.68 ± 0.12
SH 161.33 ± 14.67a 36.00 ± 7.66 39.10 ± 0.59 39.40 ± 0.37 0.90 ± 0.40
CC WAD 81.000 ± 12.71a 48.50 ± 6.63 39.00 ± 0.51 39.48 ± 0.32 2.41 ± 0.35
RS 137.14 ± 9.60a 38.86 ± 5.01 38.47 ± 0.39 39.71 ± 0.24 1.17 ± 0.26
SH 123.13 ± 8.98a 35.00 ± 4.69 38.55 ± 0.36 39.28 ± 0.23 1.17 ± 0.25

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Trop Anim Health Prod (2017) 49:323–336 333

Table 9 Interaction effect of SNP

and breed (HaeIII) on heat Breed SNP Parameters
tolerance traits of Nigerian goats
PR RR ST RT HSI

WAD GG 82.50 ± 5.33 61.24 ± 2.59 38.73 ± 0.19 39.24 ± 0.13 3.07 ± 0.13a
GA 95.82 ± 5.39 50.75 ± 2.61 38.61 ± 0.19 39.24 ± 0.13 2.36 ± 0.13a
AA 86.99 ± 7.41 57.35 ± 3.59 39.13 ± 0.26 39.21 ± 0.18 2.88 ± 0.18a
RS GG 85.67 ± 6.38 57.09 ± 3.09 38.62 ± 0.22 39.37 ± 0.15 2.83 ± 0.16a
GA 126.62 ± 5.16 40.13 ± 2.50 38.25 ± 0.18 39.17 ± 0.12 1.29 ± 0.13b
AA 103.38 ± 5.89 45.65 ± 2.86 38.41 ± 0.21 39.41 ± 0.14 1.895 ± 0.14b
SH GG 85.31 ± 6.93 39.54 ± 3.36 38.20 ± 0.24 38.89 ± 0.16 1.96 ± 0.17b
GA 126.94 ± 5.92 33.87 ± 2.87 38.68 ± 0.21 39.06 ± 0.14 1.10 ± 0.14b
AA 112.67 ± 9.09 37.17 ± 4.41 38.59 ± 0.32 39.06 ± 0.22 1.36 ± 0.22c

Means along the same column with different superscripts are significantly different (P < 0.05)

The population genetics and phylogenetic analysis have
revealed the maintenance of a greater genetic diversity, char-
acteristic population structure, and species-specific genetic
differentiation of DRB locus among the presently studied
Nigerian goats and the published caprine, bovine, and
buffaline sequences. This, according to Das et al. (2012), em-
phasizes on rigorous breeding practices focused mainly into
conservation and the possible positive influence that might
have been played by sustainable natural breeding practices
in shaping the genetic diversity of DRB locus. The interrela-
tionships among the species show a continuum in the evolu-
tionary pattern of DRB genes over various genera of mam-
mals (Singh et al. 2012). Understanding the evolutionary pat-
terns of variability in gene classes can illuminate their func-
tional characteristics (Downing et al. 2009). Kamath and Getz
(2011) reported that allele sharing among species is compati-
ble with the hypothesis that selection is acting to promote or
maintain diversity at the DRB locus. However, a more number
of alleles from each species might still give more comparative
picture of this DRB allele diversity pattern (De et al. 2011).
Marked variations were observed in the distribution of
BsaHI, AluI, HaeIII, and SacII generated genotypes in
Nigerian goats. The difference among the three Nigerian goat
breeds in the four restriction enzymes’ patterns of the DRB
second exon may be due to different breeding histories. This is
consistent with the report of Li et al. (2011) who examined the
relationship between DRB gene and Hydatidosis resistance in
Chinese sheep. While two alleles were observed in HaeIII in
the present study, Zhao et al. (2011) reported eight alleles in
Chinese goats. The difference may be due to the higher num-
ber of breeds, genetic potential, and geographical location.
However, the SacII alleles and genotypes are congruous to
those reported in sheep by Li et al. (2011). With the exception
of RS goats in AluI and WAD goats in HaeIII, other popula-
tions were in Hardy-Weinberg equilibrium (HWE) as they
were not affected by non-random mating, genetic drift, muta-
tion, genetic migration, and selection. The deviation from
HWE might not be unconnected with management systems
and mating pattern. Heterozygosity is a measure of genetic
variation or gene diversity (Baghizadeh et al. 2009) and ap-
peared high in the present study, which indicates that there is a
basis for improvement. The higher female/male ratio in the
present study is a reflection of the management of the live-
stock farmers who intend to keep more females for procre-
ation and offer for sale excess males not required for breeding.
Adaptation capacity to hot environments can be evaluated
using body temperature, respiratory rate, and heat stress index
where average relative deviations (ARD) from normal due to

Table 10 Interaction effect of

breed and sex (HaeIII) on heat Sex Breed Parameters
tolerance traits of Nigerian goats
PR RR ST RT HSI

Male WAD 89.84 ± 5.88a 57.38 ± 2.85 38.74 ± 0.21 39.18 ± 0.14 2.79 ± 0.14
RS 100.21 ± 5.69a 46.28 ± 2.76 38.53 ± 0.20 39.43 ± 0.14 2.08 ± 0.14
SH 92.88 ± 6.82a 34.21 ± 2.76 38.55 ± 0.20 38.98 ± 0.14 1.61 ± 0.14
Female WAD 87.03 ± 3.94b 55.52 ± 1.91 38.90 ± 0.14 39.27 ± 0.09 2.75 ± 0.10
RS 110.23 ± 3.60a 48.97 ± 1.75 38.33 ± 0.13 39.21 ± 0.09 1.93 ± 0.09
SH 123.73 ± 6.43a 39.50 ± 3.12 38.43 ± 0.23 39.03 ± 0.15 1.34 ± 0.16

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334
exposure to hot climates in thermal parameters of the animals
could be used in the estimation of adaptability to a hot climate
(Lallo et al. 2011; Sanni et al. 2013). Heat stress index is
commonly used as an indicator of thermal comfort. Most of
the negative effects of heat stress on animal performance are a
consequence of either physiological adaptations to regulate
body temperature or adverse consequences of failure to regu-
late body temperature (Dikmen et al. 2013). Thus, selection
for regulation of thermal indices during heat stress could in-
crease thermotolerance (Dikmen et al. 2013). The present
findings also indicated that Nigeria is rich in goat breed re-
sources that vary in their genetic potential for heat tolerance at
the DRB locus. The observed thermo-physiological responses
indicate that the northern SH and RS goat breeds have higher
adaptation capacity to hot environments than the southern
WAD breed. Similarly, Zhao et al. (2011) reported that
Southwest China is rich in goat breed resources that vary in
their genetic potential for the production of meat, milk, and
fiber; disease resistance; heat tolerance; and fecundity.
Elucidating the molecular genetic basis of adaptive traits is a
central goal of evolutionary genetics. It is believed that the
balance between the adaptive values of different gene types
under varying environments would be responsible for their
maintenance (Yakubu et al. 2014). According to Mehla et al.
(2014), understanding the biology and mechanisms of heat
stress is critical to developing approaches to ameliorate cur-
rent production issues for improving animal performance and
agriculture economics since a comprehensive explanation for
the direction of fold change and the specific genes involved in
response to acute heat stress still remains to be explored.
Therefore, the ability to maintain homeostasis under heat
stress is a valuable trait in subtropical and tropical regions
which helps to maximize utilization of animal genetic re-
sources (Fadare et al. 2012), hence the potential usefulness
of genotypes AA (BsaHI), GG, GC, and CC (AluI) and GG,
GA, AA (HaeIII) obtained in this study.
Sex is one of the factors that affect heat tolerance. The minor
sex effect observed in this study is similar to the report of
Adedeji et al. (2011) where male goats appeared more stressed
in terms of respiratory rate compared to their female counter-
parts. The interaction effect revealed separate ranking of each
factor when they are combined in the present study. Under
BsaHI, this study revealed that if selection will be done based
on a single gene, SH and RS goats with genotype AA will be
selected because they appeared to be less stressed in terms of
ST. However, genotype GG in WAD and SH goats will be
selected in terms of RT. The WAD (both male and female)
together with SH male goats appeared to have better PR under
AluI. This shows that the breeds perform differently in both
sexes. Significant results obtained for interactions of breed, sex,
and SNP genotype on heat tolerance PR suggest the sensitivity
of the expressed forms of DRB genotypes to breed differences.
Under HaeIII, selection tends to favor genotype GG in SH and
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Trop Anim Health Prod (2017) 49:323–336
genotypes GA and AA in SH and RS goats, respectively. The
WAD females, however, appeared less stressed. There is dearth
of information on the interaction effect of DRB genotypes and
thermo-physiological indices in caprine species.
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).
Compliance with ethical standards
Conflict of interest statement The authors declare that they have no
competing interests.
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