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.ResultsAn 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.ConclusionWe 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.
Highlights
Ziziphus Mill. is the best known Rhamnaceae genus of economic, ecological and cultural importance
By using Rainbow 2.0 [16], the parents’ restriction-site associated DNA (RAD) data were assembled into 177,381 contigs with a mean length of 266 bp (N50 = 266 bp, Table 1), which suggests most of the Single nucleotide polymorphism (SNP) can be used to develop SNP assays for subsequent genotyping
Compared with the reported genetic map of Chinese jujube by Qi et al in 2009 (,450 markers, 15 linkage groups (LGs), an average interval of 3.1 cM between adjacent markers) [8], the integrated linkage maps we developed for the F1 population of Z. jujuba 6 Z. acidojujuba (2,748 markers, 12 LGs and an average interval of 0.34 cM) is of very high density
Summary
Ziziphus Mill. (jujube) is the best known Rhamnaceae genus of economic, ecological and cultural importance. In 2012, the total production of Chinese jujube reached 5.4 million tons [3] with a growing area estimated 2 million hectares in China It is one of the most popularly used herbal medicines in Asia. (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. 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 Such a high-density map is still absent in the genus Ziziphus and even the family Rhamnaceae. The objective of this study was to construct a high-density linkage map using the RAD tags generated by generation sequencing
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