Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

doi:10.1186/s12864-018-4878-4

KIB OpenIR

	Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana
	Wang,Xuewen 1,2; Yang,Shuai 3; Chen,Yongdui 4; Zhang,Shumeng 2; Zhao,Qingshi 1; Li,Meng 1; Gao,Yulong 5; Yang,Long 3; Bennetzen,Jeffrey L.1,2
	2018-06-27
发表期刊	BMC Genomics
ISSN	1471-2164
卷号	19 期号:1
摘要	AbstractBackgroundSimple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.ResultsHere, we initially characterized 2,483,032 SSRs (repeat units of 1–10?bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA? software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.ConclusionsThe present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html
关键词	Genotyping technology Marker database Marker polymorphism SSR Tobacco
DOI	10.1186/s12864-018-4878-4
语种	英语
WOS记录号	BMC:10.1186/s12864-018-4878-4
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/61853
专题	中国科学院昆明植物研究所
通讯作者	Yang,Long; Bennetzen,Jeffrey L.
作者单位	1. 2. 3. 4. 5.
推荐引用方式 GB/T 7714	Wang,Xuewen,Yang,Shuai,Chen,Yongdui,et al. Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana[J]. BMC Genomics,2018,19(1).
APA	Wang,Xuewen.,Yang,Shuai.,Chen,Yongdui.,Zhang,Shumeng.,Zhao,Qingshi.,...&Bennetzen,Jeffrey L..(2018).Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana.BMC Genomics,19(1).
MLA	Wang,Xuewen,et al."Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana".BMC Genomics 19.1(2018).