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. 2017 Sep 7;7(9):3169-3176.
doi: 10.1534/g3.117.300082.

Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

Hengxing Ba  1 , Boyin Jia  1 , Guiwu Wang  1 , Yifeng Yang  1 , Gilead Kedem  2 , Chunyi Li  3
Affiliations

Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

Hengxing Ba et al. G3 (Bethesda). .

Abstract

Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (FIS >0) and low values of Hobs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.

Keywords: GenPred; Genomic Selection; SNP discovery; STACKS; Shared Data Resources; ddRAD-seq; genetic diversity; sika deer.

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Figures

Figure 1
Figure 1
Evaluation of putative SNP quality. (A) Distribution of SNP frequency on ddRAD tag positions. Distribution of the identified Ts/Tv is also illustrated. (B) Distribution of six types of substitutions. (C) Distribution of SNP frequency in major allele, minor allele, and ddRAD loci against their sequencing depth. (D) Distribution of SNP frequency of the number of SNPs in ddRAD loci tags.
Figure 2
Figure 2
Population genetic parameters for putative SNP loci. (A) Frequency of SNPs across the MAF bins. The line depicts the cumulative density function across the MAF bins. (B) Frequency of SNPs across the heterozygosity bins. (C) Frequency of SNPs across the FIS bins.
Figure 3
Figure 3
Population genetic structure. (A) STRUCTURE analysis for K = 2 and 3 for 96,188 SNPs. (B) PCA analysis for 96,188 SNPs. (C) STRUCTURE analysis for K = 2 and 3 for 13,739 SNPs. (D) PCA analysis for 13,739 SNPs.
Figure 4
Figure 4
Comparison of SNP frequency distribution between all putative SNPs and high-quality SNPs.
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