INTRODUCTION
The wild African harlequin quail (Coturnix delegorguei
delegorguei ) is endemic to Eastern and Southern Africa and is commonly
found in grassland areas with scattered bush cover (Lewis & Pomeroy,
1989). For generations, rural smallholder farmers in Kenya have hunted
quail for consumption as a complementary source of poultry protein
(Urban et al., 1986, Ogada et al., 2022). However, in addition to
continuous and uncontrolled harvesting, breeding attempts by rural
farmers, climate change, habitat destruction by humans, migration,
population bottlenecks, and inbreeding are among the main challenges
facing wild African harlequin quail in Kenya (Wamuyu et al., 2017; Ogada
et al., 2021). These factors interfere with the normal evolutionary
processes experienced by wild African harlequin quails and may influence
natural, artificial, or sexual selection (Allendorf & Hard, 2009).
In contrast, commercial quail breeds, such as the domestic Japanese
quail, have become the most commonly consumed quail species globally
since their domestication in the late 19th century and
early 20th century (Nishibori et al., 2001). The
domestic Japanese quails have undergone intense selection pressure since
their domestication through modern breeding methods aimed at increased
egg and meat production (Mills et al., 1997; Lukanov & Pavlova, 2020).
The domestication and artificial selection of the Japanese quail have
brought about genetic variation changes, altering its phenotype and
increasing its size and number of eggs laid (Lukanov & Pavlova, 2020).
The main differences between wild and domestic quail species lie in the
morphological, behavioral, and productivity characteristics (Chang et
al., 2009). In our previous study, the wild African harlequin quail meat
and eggs were found to contain higher protein content and minerals
(zinc, potassium, calcium, and iron) when compared to domestic Japanese
quail, helmeted guinea fowl, indigenous and commercial chickens
(Chepkemoi et al., 2017). Therefore, understanding the genetic
architecture of the wild African harlequin quail, among other factors,
could help elucidate this finding, among other observed traits.
Genomic regions affected by selection pressures tend to develop
signatures such as high allele frequencies, substantial linkage
disequilibrium, increased homozygous genotypes, and long haplotypes
(Nielsen, 2005; Qanbari & Simianer, 2014). Signatures of selection
tests are crucial for understanding genomes as they can provide an
accurate and deep understanding of the processes that affect population
diversity and trait selection in the genome (Oleksyk et al., 2010; Ma et
al., 2015). This study used the composite likelihood ratio test (CLR)
and integrated haplotype score (iHS) methods to detect selection
signatures. The CLR method uses site frequency spectrum (SFS) patterns
of single-nucleotide polymorphisms (Williamson et al., 2007). In
contrast, the iHS test examines the homozygosity of extended haplotypes
generated by a selective sweep (Voight et al., 2006).
Quails are increasingly becoming an essential source of poultry protein
in developing countries, thus helping to ensure food security (Jeke et
al., 2018). At present, there is no information on the impacts of
selection on the wild African harlequin quail. Furthermore, wild and
domestic quails are exposed to different selection pressures; thus, it
is important to investigate the effects of natural and artificial
selection on the quail genome. Gaining knowledge about the selection
signatures in quail genomes will form the basis for comprehending the
underlying mechanisms that influence their key traits.