The oriental turtle dove (Streptopelia orientalis) is a widespread polytypic Asian species that breeds from the Ural Mountains to the Pacific coast of the Russian Far East (Brazil 2009; Gibbs et al. 2001; Johnson et al. 2001; Lee et al. 2017). S. orientalis has been listed in the International Union for Conservation of Nature (IUCN), IUCN Red List of Threatened Species (2016), ranging from north (Heilongjiang Province) to south (Hainan Island), and from west (Xinjiang and Tibet) to east (Hong Kong and Taiwan). Although S. orientalis has not yet been classified as an endangered species, natural populations have declined dramatically in recent years because of the application of traditional Chinese medicine and commercial values. Therefore, it is urgent to perform population genetic investigation on S. orientalis to conserve and utilize the natural resources. As an important DNA marker, single nucleotide polymorphisms (SNPs) are widely used for genetic studies (Vignal et al. 2002). In this study, SNPs were developed and characterized in S. orientalis for the first time with the restriction-site associated DNA tags sequencing (RAD-seq), and will be important genetic markers for the researches on conservation genetics.

Blood was collected from 30 S. orientalis individuals from Yantai in Shandong province (37°27′N/121°30′E). Genomic DNA was extracted from blood samples using the DNeasy Blood & Tissue kit (QIAGEN, Germany) according to the manufacturer’s instructions. RAD library construction, sample indexing and pooling followed for the natural populations (Baird et al. 2008). To obtained SNP marker resources, pair-end (150-bp) sequencing was performed using Illumina HiSeq4000 (Shanghai BIOZERON Co., Ltd.), and a total of 254, 291 putative SNPs in S. orientalis was identified.

Primer v3.0 was used to design primers, 89 primer pairs successfully created. PCR reactions were performed in a 25 µl volume with GenStar PCR Mix according to the manufacturer’s instructions (GeneStar, Beijing, China). PCR amplification cycles were as follows: an initial denaturation at 94 °C for 5 min; 40 cycles of 94 °C for 30 s, annealing for 30 s (for annealing temperatures of each primer pair, see Table 1) for 30 s, and 72 °C for 30 s; and a final extension at 72 °C for 7 min. Amplified samples were purified by gel extraction and sequenced on ABI 3730 DNA Analyzer (Applied Biosystems). For validated loci, statistics including the minor allele frequency (MAF), observed heterozygosity (HO), expected heterozygosity (HE), polymorphism information content (PIC), inbreeding coefficient (FIS) and P-value representing the deviations from Hardy–Weinberg equilibrium (HWEP) were caltulated using Cervus 3.0 (Kalinowski et al. 2007).

Table 1 Characterization of 89 SNP markers in the oriental turtle dove Streptopelia orientalis
Full size table

Eighty-nine primer pairs could be amplified, and 89 SNPs located within these sequences were confirmed by Sanger sequencing. The minor allele frequency raged from 0.0417 to 0.4792 (Table 1). The observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.9583 and from 0.0816 to 0.5098, respectively. Polymorphic information content ranged from 0.0767 to 0.3746. The FIS values varied from − 0.3149 to 0.8686. Only four loci showed significant deviations from the HWE after Bonferroni correction (P < 0.05). These polymorphic SNP markers will be useful for further population genetic analysis, natural resource conservation and selective breeding of S. orientalis.