Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.)

Jin Zhao; Jianbo Jian; Guannan Liu; Jiurui Wang; Minjuan Lin; Yao Ming; Zhiguo Liu; Yingying Chen; Xiuyun Liu; Mengjun Liu

doi:10.1371/journal.pone.0109850

Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.)

PLoS One. 2014 Oct 10;9(10):e109850. doi: 10.1371/journal.pone.0109850. eCollection 2014.

Authors

Jin Zhao¹, Jianbo Jian², Guannan Liu³, Jiurui Wang⁴, Minjuan Lin⁵, Yao Ming², Zhiguo Liu⁵, Yingying Chen⁵, Xiuyun Liu⁵, Mengjun Liu⁶

Affiliations

¹ College of Life Science, Agricultural University of Hebei, Baoding, China.
² BGI-Shenzhen, Shenzhen, China.
³ College of Life Science, Nankai University, Tianjin, China.
⁴ College of Forestry, Agricultural University of Hebei, Baoding, China.
⁵ Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China.
⁶ Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China; National Agricultural Engineering Center for North Mountain Region of the Ministry of Science and Technology, Baoding, China.

Abstract

Background: Ziziphus Mill. (jujube), the most valued genus of Rhamnaceae, comprises of a number of economically and ecologically important species such as Z. jujuba Mill., Z. acidojujuba Cheng et Liu and Z. mauritiana Lam. Single nucleotide polymorphism (SNP) markers and a high-density genetic map are of great benefit to the improvement of the crop, mapping quantitative trait loci (QTL) and analyzing genome structure. However, such a high-density map is still absent in the genus Ziziphus and even the family Rhamnaceae. The recently developed restriction-site associated DNA (RAD) marker has been proven to be most powerful in genetic map construction. The objective of this study was to construct a high-density linkage map using the RAD tags generated by next generation sequencing.

Results: An interspecific F1 population and their parents (Z. jujuba Mill. 'JMS2' × Z. acidojujuba Cheng et Liu 'Xing 16') were genotyped using a mapping-by-sequencing approach, to generate RAD-based SNP markers. A total of 42,784 putative high quality SNPs were identified between the parents and 2,872 high-quality RAD markers were grouped in genetic maps. Of the 2,872 RAD markers, 1,307 were linked to the female genetic map, 1,336 to the male map, and 2,748 to the integrated map spanning 913.87 centi-morgans (cM) with an average marker interval of 0.34 cM. The integrated map contained 12 linkage groups (LGs), consistent with the haploid chromosome number of the two parents.

Conclusion: We first generated a high-density genetic linkage map with 2,748 RAD markers for jujube and a large number of SNPs were also developed. It provides a useful tool for both marker-assisted breeding and a variety of genome investigations in jujube, such as sequence assembly, gene localization, QTL detection and genome structure comparison.

Publication types

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

MeSH terms

Alleles
Genetic Linkage*
Genome, Plant*
High-Throughput Nucleotide Sequencing
Polymorphism, Single Nucleotide*
Quantitative Trait Loci
Ziziphus / genetics*

Grants and funding

This study was supported by grants from National Science and Technology Support Plan of China (No. 2013BAD14B03), Provincial Key Technology R&D Program of Hebei of China (No. 11230606D-6). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.