Fan Wei, Zong Jie, Luo Zhijing, Chen Mingjiao, Zhao Xiangxiang, Zhang Dabing, Qi Yiping, Yuan Zheng
State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Novel Bioinformatics Company, Shanghai, China.
PLoS One. 2016 Jan 22;11(1):e0147187. doi: 10.1371/journal.pone.0147187. eCollection 2016.
Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.
快速准确的全基因组标记检测对于标记辅助育种和功能基因组学研究至关重要。在本研究中，我们开发了一款集成软件AgroMarker Finder（AMF：http://erp.novelbio.com/AMF），用于提供图形用户界面（GUI），以促进最近开发的水稻限制性内切酶相关DNA（RAD）测序数据分析。通过应用AMF，在水稻品种JP69和交源5A之间共检测到90,743个高质量标记（82,878个单核苷酸多态性（SNP）和7,865个插入缺失（InDel））。所鉴定标记的密度对于SNP标记为每千碱基0.2个，对于InDel标记为每千碱基0.02个。测序验证表明，AMF全基因组标记检测的准确性为93%。此外，发现82个SNP和31个InDel的验证子集与117个重要农艺性状基因紧密连锁，为后续标记辅助选择（MAS）和品种鉴定提供了依据。此外，我们从31个经过验证的InDel标记中选择了12个标记来鉴定交源优69品种的种子真实性，并且我们还鉴定了10个与香味基因BADH2紧密连锁的标记，以尽量减少无香075（BADH2供体）/嘉长1重组体选择中的连锁累赘。因此，该软件为从RAD-seq数据中鉴定标记提供了一种有效方法，并且将成为植物MAS和品种保护的有价值工具。
