Knowledge Management System Of Institute Of Botany,CAS
| SorGSD: a sorghum genome SNP database | |
Luo, Hong9; Zhao, Wenming1; Wang, Yanqing1; Xia, Yan; Wu, Xiaoyuan; Zhang, Limin; Tang, Bixia1; Zhu, Junwei1; Fang, Lu1; Du, Zhenglin1; Bekele, Wubishet A.; Tai, Shuaishuai3; Jordan, David R.; Godwin, Ian D.; Snowdon, Rod J.; Mace, Emma S.; Jing, Hai-Chun ; Luo, Jingchu7,8
| |
| 2016 | |
| 发表期刊 | BIOTECHNOLOGY FOR BIOFUELS
 |
| ISSN | 1754-6834 |
| 卷号 | 9 |
| 摘要 | Background: Sorghum (Sorghum bicolor) is one of the most important cereal crops globally and a potential energy plant for biofuel production. In order to explore genetic gain for a range of important quantitative traits, such as drought and heat tolerance, grain yield, stem sugar accumulation, and biomass production, via the use of molecular breeding and genomic selection strategies, knowledge of the available genetic variation and the underlying sequence polymorphisms, is required. Results: Based on the assembled and annotated genome sequences of Sorghum bicolor (v2.1) and the recently published sorghum re-sequencing data, similar to 62.9 M SNPs were identified among 48 sorghum accessions and included in a newly developed sorghum genome SNP database SorGSD (http://sorgsd.big.ac.cn). The diverse panel of 48 sorghum lines can be classified into four groups, improved varieties, landraces, wild and weedy sorghums, and a wild relative Sorghum propinquum. SorGSD has a web-based query interface to search or browse SNPs from individual accessions, or to compare SNPs among several lines. The query results can be visualized as text format in tables, or rendered as graphics in a genome browser. Users may find useful annotation from query results including type of SNPs such as synonymous or non-synonymous SNPs, start, stop of splice variants, chromosome locations, and links to the annotation on Phytozome (www.phytozome.net) sorghum genome database. In addition, general information related to sorghum research such as online sorghum resources and literature references can also be found on the website. All the SNP data and annotations can be freely download from the website. Conclusions: SorGSD is a comprehensive web-portal providing a database of large-scale genome variation across all racial types of cultivated sorghum and wild relatives. It can serve as a bioinformatics platform for a range of genomics and molecular breeding activities for sorghum and for other C-4 grasses. |
| 关键词 | Sorghum Bio-energy plant Genome variation SNPs Database curation |
| 学科领域 | Biotechnology & Applied Microbiology ; Energy & Fuels |
| DOI | 10.1186/s13068-015-0415-8 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS关键词 | WIDE ASSOCIATION ; DISCOVERY ; MODEL ; FRAMEWORK ; SYSTEM ; MAIZE ; SWEET |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000367708200001 |
| 出版者 | BMC |
| 文献子类 | Article |
| 出版地 | LONDON |
| 资助机构 | National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31461143023, 31271797] ; National Science and Technology Support Program [2015BAD15B03, 2013BAD22B01] ; Sino-Africa Centre of CAS International Outreach Initiatives |
| 作者邮箱 | hcjing@ibcas.ac.cn ; luojc@pku.edu.cn |
| 作品OA属性 | gold, Green Published |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/25283 |
| 专题 | 中科院北方资源植物重点实验室 |
| 作者单位 | 1.Chinese Acad Sci, Genom & Mol Breeding Biofuel Crops, Key Lab Plant Resources, Inst Bot, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Beijing Inst Genom, Beijing 100101, Peoples R China 3.Bekele, Wubishet A.; Snowdon, Rod J.] Univ Giessen, Dept Plant Breeding, D-35390 Giessen, Germany 4.BGI Shenzhen, Shenzhen 518083, Peoples R China 5.Jordan, David R.] Univ Queensland, Queensland Alliance Agr & Food Innovat, Warwick, Qld 4370, Australia 6.Godwin, Ian D.] Univ Queensland, Sch Agr & Food Sci, Brisbane, Qld 4072, Australia 7.Mace, Emma S.] DAFF, Warwick, Qld 4370, Australia 8.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China 9.Peking Univ, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China 10.Univ Wageningen & Res Ctr, Lab Bioinformat, Wageningen, Netherlands |
| 推荐引用方式 GB/T 7714 | Luo, Hong,Zhao, Wenming,Wang, Yanqing,et al. SorGSD: a sorghum genome SNP database[J]. BIOTECHNOLOGY FOR BIOFUELS,2016,9. |
| APA | Luo, Hong.,Zhao, Wenming.,Wang, Yanqing.,Xia, Yan.,Wu, Xiaoyuan.,...&Luo, Jingchu.(2016).SorGSD: a sorghum genome SNP database.BIOTECHNOLOGY FOR BIOFUELS,9. |
| MLA | Luo, Hong,et al."SorGSD: a sorghum genome SNP database".BIOTECHNOLOGY FOR BIOFUELS 9(2016). |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Luo-2016-SorGSD_ a s（989KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。
修改评论