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

	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
刊名	peerj
	2016-02-22
卷号	4
关键词	Genome Jujube Population genetics Microsatellite SSR abundance SSR primers
英文摘要	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.
WOS标题词	science & technology
类目[WOS]	multidisciplinary sciences
研究领域[WOS]	science & technology - other topics
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
WOS记录号	WOS:000370984300010
内容类型	期刊论文
源URL	[http://ir.nwipb.ac.cn/handle/363003/5784]
专题	西北高原生物研究所_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).