Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)

doi:10.7717/peerj.1735

NWIPB OpenIR

	Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)
	Fu, Peng-cheng 1; Zhang, Yan-zhao 1; Ya, Hui-yuan 1; Gao, Qing-bo 2
	2016-02-22
发表期刊	PEERJ
卷号	4
文章类型	Article
摘要	Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polyrnorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.
关键词	Genome Jujube Population Genetics Microsatellite Ssr Abundance Ssr Primers
WOS标题词	Science & Technology
DOI	10.7717/peerj.1735
关键词[WOS]	SIMPLE SEQUENCE REPEAT ; DIVERSITY ; CULTIVARS ; MICROSATELLITES ; SOFTWARE ; BIOLOGY ; WINDOWS ; ORIGIN ; LINUX ; DNA
收录类别	SCI
语种	英语
项目资助者	National Natural Science Foundation of China(31400322 ; Joint Funds of the National Natural Science Foundation of China(U1204307) ; 31270270 ; 31400602)
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000370984300010
引用统计	被引频次：13[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/5784
专题	中国科学院西北高原生物研究所
作者单位	1.Luoyang Normal Univ, Coll Life Sci, Luoyang, Peoples R China 2.Chinese Acad Sci, Key Lab Adaptat & Evolut Plateau Biota, Northwest Inst Plateau Biol, Xining, Peoples R China
推荐引用方式 GB/T 7714	Fu, Peng-cheng,Zhang, Yan-zhao,Ya, Hui-yuan,et al. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)[J]. PEERJ,2016,4.
APA	Fu, Peng-cheng,Zhang, Yan-zhao,Ya, Hui-yuan,&Gao, Qing-bo.(2016).Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.).PEERJ,4.
MLA	Fu, Peng-cheng,et al."Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)".PEERJ 4(2016).