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

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.

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Acknowledgments

This study was supported by the Fundamental Research Funds for the Central Universities (No. 2014YB074) and the Key Project from the Government of Shaanxi Province (No. 2013KTZB02-03, 2015SZS-10 and 2012cxyl-2). We also thank for the graduate students Weikang Wang, Miaomiao Sun, and Shuyi Zhang in jujube research group, and Mr. Jun Zhang for the plant material preparation and DNA extraction.

Data archiving statement

The supplementary materials mentioned in the manuscript can be found in Online Resources ESM_1 through ESM_12. Detailed sequencing information of the SNP markers mapped onto the two parent maps can be found in Online Resources 7 and 8 (ESM_7 and ESM_8). The raw sequencing data reported here have been submitted to the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI); related accession numbers are listed in Online Resource 13 (ESM_13).

Author information

Correspondence to Xingang Li or Jian Huang.

Additional information

Communicated by D. Grattapaglia

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Zhang, Z., Wei, T., Zhong, Y. et al. Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology. Tree Genetics & Genomes 12, 76 (2016). https://doi.org/10.1007/s11295-016-1032-9

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Keywords

  • Genetic map
  • Ziziphus jujuba Mill.
  • Genotyping by sequencing (GBS)
  • SNP