Demographic history and genetic diversity of wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya

Abstract

Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mitochondrial DNA (mtDNA) control region fragment and 119,339 single nucleotide polymorphisms (SNPs) from genotyping‐by‐sequencing (GBS) data. Genetic diversity analyses revealed that the genetic variation in wild African harlequin quails was predominantly among individuals than populations. Demographic analyses indicated a signal of rapid demographic expansion, and the estimated time since population expansion was found to be 150,000–350,000 years ago, corresponding to around the Pliocene–Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. These results provide the first account of the genetic diversity of wild African harlequin quails of Siaya, thereby creating a helpful foundation in their biodiversity conservation.

Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds

“…To date, there have been a number of investigations focusing on the genetic diversity in quails. These studies were mainly related to the assessment of the genotypes of domestic and wild quails in order to characterize the genetic structure of populations in these species [22,72,73], as well as the issues of their hybridization in the wild [74][75][76]. Most of the work in this area was executed using microsatellite and mtDNA markers [72][73][74][75][76][77].…”

“…For example, Mathur and DeWoody [90] examined the genetic diversity of three populations of the wild Montezuma quail (Cyrtonyx montezumae) using whole-genome sequencing data from 74 quails. Ogada et al [22] utilized both mtDNA and GBS analyses to investigate the genetic diversity and demographic history of wild African harlequin quail populations of Siaya County. In the current study, we demonstrated the effectiveness of SNPs, as the currently most used molecular markers, and the GBS approach for a genomewide comparative assessment of different breeds of domestic quail.…”

“…Genotyping by sequencing (GBS), one of the restriction enzyme-based enrichment approaches designed initially for plants [16], is a promising strategy for reducing the financial burden of selection strategies via high sample multiplexing, focusing the sequenced genome areas on randomly distributed read tags [17]. Being a relatively affordable and widely applicable substitute for concurrent single-nucleotide polymorphism (SNP) mining and genotyping in plants (e.g., [16,18,19]), GBS is also increasingly being used in animals (e.g., [17,[19][20][21][22]). Indeed, there was a recent report that GBS has been utilized for evaluating demographic history and genetic divergence in wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya [22].…”

“…Being a relatively affordable and widely applicable substitute for concurrent single-nucleotide polymorphism (SNP) mining and genotyping in plants (e.g., [16,18,19]), GBS is also increasingly being used in animals (e.g., [17,[19][20][21][22]). Indeed, there was a recent report that GBS has been utilized for evaluating demographic history and genetic divergence in wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya [22]. Ravagni et al [23] employed GBS to explore the evolutionary history of an island endemic, the common quail (Coturnix coturnix) in the Azores archipelago.…”

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

“…The lack of commercial SNP arrays for Japanese quail makes it difficult to search for SNPs and identify genes associated with traits important for breeding, suggesting other SNP genotyping approaches [ 43 ]. Recently, we applied, for the first time, genotyping-by-sequencing (GBS) technology [ 44 , 45 ] in Japanese quails to generate multiple genome-wide SNP markers for executing GWAS of growth dynamics [ 43 ] and characterizing within- and between-breed genetic diversity [ 46 ].…”