Development and characterization of 31 SNP markers for the Crested ibis ( Nipponia nippon )
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TECHNICAL NOTE
Development and characterization of 31 SNP markers for the Crested ibis (Nipponia nippon) Wenhui Niu1 · Yongjie Huang2 · Chenglin Zhang1 · Tianchun Pu1 · Yan Lu1 · Ting Jia1 · Yuyan You1 · Yang Du1 · Yu Mao1 · Changqing Ding2 Received: 24 September 2020 / Accepted: 1 October 2020 © Springer Nature B.V. 2020
Abstract 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. Keywords Crested ibis · SNP markers · Population genetic analysis · Restriction-site associated DNA (RAD) The Crested ibis (Nipponia nippon) was once widely distributed throughout East Asia. Due to the habitat loss, food shortage and over-hunting, this species became extinct over nearly all of its former ranges since the late nineteenth century (Ding 2004). In 1981, the last seven individuals were rediscovered in Yangxian County, Shaanxi Province of China. These fortunate survivors have been successfully rescued by efforts through in situ conservation, artificial rearing and reintroduction, leading to the establishment of several captive flocks and one wild population with around 1000 birds (Wang et al. 2014). However, this single wild population, though large enough, cannot guarantee the future of this species (Ding 2010) unless an effective conservation genetics program is installed to monitor the limited, but essential, adaptive variations among the current breeding stocks.
Wenhui Niu and Yongjie Huang have contributed equally to this manuscript. * Changqing Ding [email protected] 1
Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, P. R. China
School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
2
Using traditional molecular markers including microsatellites and mtDNA sequences, some neutral genetic variations in several flocks of the Crested ibis were identified (He et al. 2006, 2013). To assess the level of the adaptive and functional variations essential to the survival and successful recovery of this species, genome-wide screening of SNPs using next generation sequencing technologies (Vignal et al. 2002) is warranted. In this study, we developed and characterized SNP markers in Crested ibis using restriction-site associated DNA (RAD) sequencing. We sequenced the blood samples of Crested ib
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