Development and characterization of novel microsatellite markers for the Common Pheasant (Phasianus colchicus) using RAD-seq

Abstract

Background:The Common Pheasant (Phasianus colchicus) Linnaeus, 1758 is the most widespread pheasant in the world and widely introduced as a game bird. Increasing needs for conservation genetics and management of both wild and captive populations require permanent genetic resources, such as polymorphic microsatellites in order to genotype individuals and populations. Methods:In this study, 7598 novel polymorphic microsatellites for the Common Pheasant were isolated using a RAD-seq approach at an Illumina high-throughput sequencing platform. A panel of ten novel microsatellites and three existing ones from the chicken genome were multiplexed and genotyped on a set of 90 individuals of Common Pheasants (representing nine subspecies and ten individuals each) and 10 individuals of the Green Pheasant (P. versicolor).Results: These 13 microsatellites exhibited moderate to high levels of polymorphism, with the number of alleles per locus ranging from 2 to 8 and expected heterozygosities from 0.049 to 0.905. The first analysis of the genetic structure of subspecies/populations using a Bayesian clustering approach, implemented in STRUCTURE, showed two genetic clusters, corresponding to both the Green and the Common Pheasant, with further evidence of subpopulation structuring within the Common Pheasants. Conclusion:These markers are useful genetic tools for sustainable uses and evolutionary studies in these two Phasianus pheasants and probably other closely related game birds.

Phylogeography of the Common Pheasant Phasianus colchicus

“…To analyse further the boundaries and genetic admixture among subspecies, efforts to quantify morphology and to genotype populations using high‐polymorphic genetic markers will be necessary (Wang et al . ).…”

Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Nephelium lappaceum L.) germplasm

“…Notably, the implementation of RAD sequencing-based Illumina platform contributes to the generation of comparatively long paired-end sequencing reads (100–150 bp). This platform is also cost-efficient and adequate for the development of microsatellites ( Castoe et al., 2012 ; Wang et al., 2017 ). However, a reference genome is not required in this method and it enables the assembly of de-novo genome ( Willing et al., 2011 ; Wang et al., 2017 ).…”

Peer Review #1 of "Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites (v0.2)"

“…Because of their relatively high level of polymorphism, repeatability in genotyping and high PCR amplification success, microsatellites are advantageous genetic tool to address conservation and behavioural genetic patterns in threatened species towards their conservation and management issues (Faria et al, 2016;Wang et al, 2017). A key part of microsatellite-based conservation genetics is to develop either species-specific or cross-species primer sets, with the development of next-generation sequencing, the development of reliable microsatellites are no longer an timeconsuming task, even for birds that have few known microsatellite loci in their genomes (Castoe et al, 2012;Wang et al, 2017;Yang et al, 2017).…”