Development and characterization of 31 SNP markers for the Crested ibis (Nipponia nippon)

Single nucleotide polymorphisms (SNPs), known as the third-generation molecular markers, are becoming popular in molecular ecology studies. The rapid development of next generation sequencing technologies allow identifying large numbers of SNP markers that can be used in conservation genetics. Based on the genome resequencing dataset of Crested ibis (Nipponia nippon), we developed 31 polymorphic SNP markers using the restriction-site associated DNA (RAD) sequencing. The minor allele frequency per locus varied from 0.176 to 0.485, while the observed and expected heterozygosity varied from 0.118 to 0.794 and from 0.295 to 0.507, respectively. Three loci showed significant departures from Hardy–Weinberg equilibrium. These SNP markers could be useful in future population genetic analysis of Crested ibis.