Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

Wei Fan; Jie Zong; Zhijing Luo; Mingjiao Chen; Xiangxiang Zhao; Dabing Zhang; Yiping Qi; Zheng Yuan

doi:10.1371/journal.pone.0147187

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

PLoS One. 2016 Jan 22;11(1):e0147187. doi: 10.1371/journal.pone.0147187. eCollection 2016.

Authors

Wei Fan¹, Jie Zong², Zhijing Luo¹, Mingjiao Chen¹, Xiangxiang Zhao³, Dabing Zhang^{1

3

4}, Yiping Qi⁵, Zheng Yuan^{1

3}

Affiliations

¹ 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.
² Novel Bioinformatics Company, Shanghai, China.
³ Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Jiangsu, China.
⁴ Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia.
⁵ Department of Biology, East Carolina University, Greenville, North Carolina, United States of America.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't
Validation Study

MeSH terms

DNA / genetics*
Genes, Plant
Oryza / genetics*
Plant Breeding*
Polymorphism, Single Nucleotide*
Software*

Substances

DNA

Grants and funding

This work was supported by the Funds from the EU FP7 project (DECATHLON, 613908), Project on Breeding from Agriculture Commission of Shanghai (2013-13, 2014-1-3), National Natural Science Foundation of China (31470397, 31270222, 31230051 and 31110103915), Key Project on Basic Research from Science and Technology Commission of Shanghai (14JC1403900, 14391917100), and China Talents of Discipline to Universities (111 Project, B14016). Novel Bioinformatics Company provided support in the form of salaries for authors [JZ], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.