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; Boyin Jia; Guiwu Wang; Yifeng Yang; Gilead Kedem; Chunyi Li

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

G3 (Bethesda). 2017 Sep 7;7(9):3169-3176. doi: 10.1534/g3.117.300082.

Authors

Hengxing Ba¹, Boyin Jia¹, Guiwu Wang¹, Yifeng Yang¹, Gilead Kedem², Chunyi Li³

Affiliations

¹ State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
² GENEWIZ Inc., South Plainfield, New Jersey 07080.
³ State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China lichunyi1959@163.com.

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 (F_IS >0) and low values of H_obs, 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
China
Deer / genetics*
Gene Frequency
Genetic Variation*
Genetics, Population
Genome*
Genome-Wide Association Study*
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA