Abstract:
The indigenous guinea fowl plays a vital role in the agricultural industry as both its meat and
eggs are healthy, tasty and serve as an important protein source for consumers. However,
genetic progress on this bird has been partially hindered by the absence of polymorphic
markers, especially microsatellites. Therefore, this study developed for the first time original
microsatellite markers for this economically important species. The 454 sequencing technique
(next-generation sequencing), which is known to eliminate the time consuming cloning step in
the traditional microsatellite marker development method, was used in this study. A genomic
library was constructed from DNA extracted from the blood of a female guinea fowl, using the
next-generation sequencer. A total of 105,015 reads with an average read length of 393 bp
containing 1,234 possible microsatellite sites were obtained. One hundred and fifty four
primers were designed from the flanking regions of the microsatellites and tested at 55 °C and
60 °C in a polymerase chain reaction using DNA from four unrelated guinea fowls. One
hundred and twenty two of these primers showed clear amplification patterns. Polymorphism
of 38 of the optimized markers was tested with DNA samples from 32 unrelated individuals
and 31 of them were polymorphic. For the 31 polymorphic loci, the observed number of alleles
ranged from 2 to 9 (mean 3.39) with allele sizes ranging from 94 bp to 286 bp, while the
effective number of alleles ranged from 1.03 to 4.97 (mean 2.04). The observed (HO) and
expected heterozygosities (He) ranged from 0.033 to 1.000 (mean 0.396) and 0.033 to 0.799
(mean 0.419), respectively. Nine loci significantly deviated from Hardy-Weinberg Equilibrium
(p < 0.05) after Bonferroni correction. The mean fixation index (F) for all 31 loci was 0.052 (-1
to 0.71) while the average probability of identity (PI) was 0.43. Shannon’s Index ranged from
0.085 to 1.821 (mean 0.750). The polymorphism information content (PIC) of the 31 markers
averaged 0.3689 (0.0329 to 0.7735) with 29% of them being highly informative (PIC > 0.50),
35.5% being reasonably informative (0.50 > PIC > 0.25), and 35.5% being slightly informative (PIC < 0.25). The results of this study would serve as baseline information for
genetic diversity studies, genetic linkage mapping, quantitative trait loci analysis as well as
inform breeding strategies for the improvement and conservation in both domestic and wild
populations of the species.
