Cargando…
Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding
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 recent...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723255/ https://www.ncbi.nlm.nih.gov/pubmed/26799713 http://dx.doi.org/10.1371/journal.pone.0147187 |
_version_ | 1782411483402993664 |
---|---|
author | Fan, Wei Zong, Jie Luo, Zhijing Chen, Mingjiao Zhao, Xiangxiang Zhang, Dabing Qi, Yiping Yuan, Zheng |
author_facet | Fan, Wei Zong, Jie Luo, Zhijing Chen, Mingjiao Zhao, Xiangxiang Zhang, Dabing Qi, Yiping Yuan, Zheng |
author_sort | Fan, Wei |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4723255 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-47232552016-01-30 Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding Fan, Wei Zong, Jie Luo, Zhijing Chen, Mingjiao Zhao, Xiangxiang Zhang, Dabing Qi, Yiping Yuan, Zheng PLoS One Research Article 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. Public Library of Science 2016-01-22 /pmc/articles/PMC4723255/ /pubmed/26799713 http://dx.doi.org/10.1371/journal.pone.0147187 Text en © 2016 Fan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article 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 |
title | Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding |
title_full | Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding |
title_fullStr | Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding |
title_full_unstemmed | Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding |
title_short | Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding |
title_sort | development of a rad-seq based dna polymorphism identification software, agromarker finder, and its application in rice marker-assisted breeding |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723255/ https://www.ncbi.nlm.nih.gov/pubmed/26799713 http://dx.doi.org/10.1371/journal.pone.0147187 |
work_keys_str_mv | AT fanwei developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT zongjie developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT luozhijing developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT chenmingjiao developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT zhaoxiangxiang developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT zhangdabing developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT qiyiping developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding AT yuanzheng developmentofaradseqbaseddnapolymorphismidentificationsoftwareagromarkerfinderanditsapplicationinricemarkerassistedbreeding |