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

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    Author
    Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng
    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 soft- ware, 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 mark- ers (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. Further- more, 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 recombi- nants selection. Therefore, this software provides an efficient approach for marker identifi- cation from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.
    URI
    http://hdl.handle.net/10342/8501
    Date
    2016-01-22
    Citation:
    APA:
    Fan, Wei, & Zong, Jie, & Luo, Zhijing, & Chen, Mingjiao, & Zhao, Xiangxiang, & Zhang, Dabing, & Qi, Yiping, & Yuan, Zheng. (January 2016). Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLOS One, (11:1), p.. Retrieved from http://hdl.handle.net/10342/8501

    Display/Hide MLA, Chicago and APA citation formats.

    MLA:
    Fan, Wei, and Zong, Jie, and Luo, Zhijing, and Chen, Mingjiao, and Zhao, Xiangxiang, and Zhang, Dabing, and Qi, Yiping, and Yuan, Zheng. "Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding". PLOS One. 11:1. (.), January 2016. April 18, 2021. http://hdl.handle.net/10342/8501.
    Chicago:
    Fan, Wei and Zong, Jie and Luo, Zhijing and Chen, Mingjiao and Zhao, Xiangxiang and Zhang, Dabing and Qi, Yiping and Yuan, Zheng, "Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding," PLOS One 11, no. 1 (January 2016), http://hdl.handle.net/10342/8501 (accessed April 18, 2021).
    AMA:
    Fan, Wei, Zong, Jie, Luo, Zhijing, Chen, Mingjiao, Zhao, Xiangxiang, Zhang, Dabing, Qi, Yiping, Yuan, Zheng. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLOS One. January 2016; 11(1) . http://hdl.handle.net/10342/8501. Accessed April 18, 2021.
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