Rapid microsatellite development for tree peony and its implications

doi:10.1186/1471-2164-14-886

	Rapid microsatellite development for tree peony and its implications
	Gao, Zhimin 1; Wu, Jie 2; Liu, Zheng'an ; Wang, Liangsheng; Ren, Hongxu ; Shu, Qingyan
	2013
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	14
摘要	Background: Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as 'junk' DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences. Results: In this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1-4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)(n), with (G/C)(n) less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21-30 and 101-110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers. Conclusions: The results of our large-scale SSR marker development using tree peony are valuable for investigating plant genomic structural evolution and elucidating phenotypic variation in this species during its evolution and artificial selection. The newly identified SSRs should be useful for genetic linkage map construction, QTL mapping, gene location and cloning, and molecular marker-assisted breeding. In addition, the genome-wide marker resources generated in this study should aid genomic studies of tree peony and related species.
关键词	Microsatellite Next-generation sequencing Tree peony Ornamental SSR marker
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/1471-2164-14-886
收录类别	SCI
语种	英语
WOS关键词	SEQUENCE REPEATS ; MARKERS ; LOCI ; IDENTIFICATION ; DIVERSITY ; MECHANISM ; DISCOVERY ; LIBRARIES ; PROGRAM ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000329365500001
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of China(National Natural Science Foundation of China (NSFC)) ; National High Technology Research and Development Program of China (863 Program)(National High Technology Research and Development Program of China)
作品OA属性	gold, Green Published
引用统计	被引频次：35[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27796
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing Bot Garden, Beijing 100093, Peoples R China 2.Int Ctr Bamboo & Rattan, Key Lab Sci & Technol Bamboo & Rattan, Beijing 100102, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Gao, Zhimin,Wu, Jie,Liu, Zheng'an,et al. Rapid microsatellite development for tree peony and its implications[J]. BMC GENOMICS,2013,14.
APA	Gao, Zhimin,Wu, Jie,Liu, Zheng'an,Wang, Liangsheng,Ren, Hongxu,&Shu, Qingyan.(2013).Rapid microsatellite development for tree peony and its implications.BMC GENOMICS,14.
MLA	Gao, Zhimin,et al."Rapid microsatellite development for tree peony and its implications".BMC GENOMICS 14(2013).

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