title: Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.).
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: College of Life Science, Agricultural University of Hebei, Baoding, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhao
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Jian
authors.affiliation: College of Life Science, Nankai University, Tianjin, China.
authors.forename: Guannan
authors.initials: G
authors.lastname: Liu
authors.affiliation: College of Forestry, Agricultural University of Hebei, Baoding, China.
authors.forename: Jiurui
authors.initials: J
authors.lastname: Wang
authors.affiliation: Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China.
authors.forename: Minjuan
authors.initials: M
authors.lastname: Lin
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Ming
authors.affiliation: Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, China.
authors.forename: Xiuyun
authors.initials: X
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Mengjun
authors.initials: M
authors.lastname: Liu
mesh_terms: D000483:Alleles; D008040:Genetic Linkage; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D031957:Ziziphus / Q000235:genetics*