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

BMC Genomics

Research Article

Hui Zhi¹  Meicheng Zhao¹  Chanjuan Tang¹  Xiaotong Liu¹  Lifang Yang¹  Shuo Zhang¹  Yang Chai¹  Guanqing Jia¹  Wen Li²  Lufeng Qie³  Hailong Wang³  Xingke Fan³  Lin Li³  Xianmin Diao³  Jing Li³  Xue Zhang³  Yingtao Li³  Qiang Zhao⁴  Ning Zhang⁵ 

[1] Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;College of Agronomy, Shanxi Agricultural University, 030801, Jinzhong, China;Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;College of Life Science, Hebei Normal University, 050012, Shijiazhuang, China;National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200233, Shanghai, China;National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China;

关键词: Microsatellite marker;    SSR development;    Polymorphism;    Setaria italica;   

DOI  :  10.1186/1471-2164-15-78

 received in 2013-09-03, accepted in 2014-01-27,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundFoxtail 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 C4 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.ResultA 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.ConclusionsA 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.

【 授权许可】

Unknown   
© Zhang et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.