Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]

doi:10.1186/1471-2164-15-78

	Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]
	Zhang, Shuo 1; Tang, Chanjuan 1; Zhao, Qiang 2; Li, Jing 1,4; Yang, Lifang 1; Qie, Lufeng 1,4; Fan, Xingke 1,4; Li, Lin 1,4; Zhang, Ning 3; Zhao, Meicheng 1
刊名	BMC GENOMICS
	2014
卷号	15 页码:-
关键词	Microsatellite marker SSR development Polymorphism Setaria italica
ISSN号	1471-2164
DOI	10.1186/1471-2164-15-78
通讯作者	Zhang, Shuo
英文摘要	Background: Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C-4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.Result: A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1' by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei's genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.Conclusions: A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; GENETICS & HEREDITY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000332573700001
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4940]
专题	作物科学研究所_种质资源保存与研究中心
作者单位	1.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Ctr Gene Res, Shanghai 200233, Peoples R China 3.Chinese Acad Sci, Inst Genet & Dev Biol, Natl Ctr Plant Gene Res, State Key Lab Plant Genom, Beijing 100101, Peoples R China 4.Hebei Normal Univ, Coll Life Sci, Shijiazhuang 050012, Peoples R China 5.Shanxi Agr Univ, Coll Agron, Jinzhong 030801, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Shuo,Tang, Chanjuan,Zhao, Qiang,et al. Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.][J]. BMC GENOMICS,2014,15:-.
APA	Zhang, Shuo.,Tang, Chanjuan.,Zhao, Qiang.,Li, Jing.,Yang, Lifang.,...&Diao, Xianmin.(2014).Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.].BMC GENOMICS,15,-.
MLA	Zhang, Shuo,et al."Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]".BMC GENOMICS 15(2014):-.