Affordable Access

Access to the full text

Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology

Authors
  • Zhang, Zhong1, 2, 3
  • Wei, Tianjun4
  • Zhong, Ying5
  • Li, Xingang1, 2, 3
  • Huang, Jian1, 3
  • 1 Northwest A&F University, College of Forestry, Yangling, Shaanxi, 712100, China , Yangling (China)
  • 2 State Forestry Administration, Research Centre for Jujube Engineering and Technology, Yangling, Shaanxi, 712100, China , Yangling (China)
  • 3 Key Comprehensive Laboratory of Forestry, Shaanxi Province, Yangling, Shaanxi, 712100, China , Yangling (China)
  • 4 Ningxia Academy of Agricultural and Forestry Science, Institute of Gemplasm Resource, Yinchuan, Ningxia, 750000, China , Yinchuan (China)
  • 5 Novogene Bioinformatics Institute, Beijing, 100000, China , Beijing (China)
Type
Published Article
Journal
Tree Genetics & Genomes
Publisher
Springer Berlin Heidelberg
Publication Date
Jul 15, 2016
Volume
12
Issue
4
Identifiers
DOI: 10.1007/s11295-016-1032-9
Source
Springer Nature
Keywords
License
Yellow

Abstract

The Chinese jujube (Ziziphus jujuba Mill., 2n = 2 × = 24), one of the most popular fruit trees in China, is widely cultivated and utilized in Asia. High-density genetic linkage maps are valuable resources for molecular breeding and functional genomics; however, they are still under-developed for the jujube. The genotyping by sequencing (GBS) strategy could be an efficient and cost-effective tool for single nucleotide polymorphism (SNP) discovery based on the sequenced jujube genome. Here, we report a new high-density genetic map constructed using GBS technology. An F1 population with 145 progenies and their parents (‘Dongzao’ × ‘Zhongningyuanzao’) were sequenced on the Illumina HiSeq 4000 platform. In total, 79.8 Gb of raw data containing 256,708,177 paired-end reads were generated. After data filtering and SNP genotyping, 40,372 polymorphic SNP markers were developed between the parents and 2540 (1756 non-redundant) markers were mapped onto the integrated genetic linkage map. The map spanned 1456.53 cM and was distributed among 12 linkage groups, which is consistent with the haploid chromosome number of the jujube. The average marker interval was 0.88 cM. The genetic map allowed us to anchor 224 Mb (63.7 %) of scaffolds from the sequenced ‘Junzao’ genome, containing 52 newly anchored scaffolds, which extended the genome assembly by 7 Mb. In conclusion, GBS technology was applied efficiently for SNP discovery in this study. The high-density genetic map will serve as a unique tool for molecular-assisted breeding and genomic studies, which will contribute to further research and improvement of the jujube in the near future.

Report this publication

Statistics

Seen <100 times