Luo Hong, Zhao Wenming, Wang Yanqing, Xia Yan, Wu Xiaoyuan, Zhang Limin, Tang Bixia, Zhu Junwei, Fang Lu, Du Zhenglin, Bekele Wubishet A, Tai Shuaishuai, Jordan David R, Godwin Ian D, Snowdon Rod J, Mace Emma S, Jing Hai-Chun, Luo Jingchu
Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
Laboratory of Bioinformatics, Wageningen University and Research Centre, Wageningen, The Netherlands.
Biotechnol Biofuels. 2016 Jan 7;9:6. doi: 10.1186/s13068-015-0415-8. eCollection 2016.
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.
Based on the assembled and annotated genome sequences of Sorghum bicolor (v2.1) and the recently published sorghum re-sequencing data, ~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.
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 C4 grasses.
高粱（Sorghum bicolor）是全球最重要的谷类作物之一，也是用于生物燃料生产的潜在能源植物。为了通过分子育种和基因组选择策略探索一系列重要数量性状的遗传增益，如耐旱性、耐热性、籽粒产量、茎中糖分积累和生物量生产，需要了解可用的遗传变异以及潜在的序列多态性。
基于双色高粱（v2.1）组装和注释的基因组序列以及最近公布的高粱重测序数据，在48份高粱种质中鉴定出约6290万个单核苷酸多态性（SNP），并纳入新开发的高粱基因组SNP数据库SorGSD（http://sorgsd.big.ac.cn）。48个高粱品系的多样化群体可分为四组：改良品种、地方品种、野生和杂草高粱以及野生近缘种拟高粱（Sorghum propinquum）。SorGSD有一个基于网络的查询界面，可用于搜索或浏览单个种质的SNP，或比较多个品系之间的SNP。查询结果可以以表格形式的文本格式可视化，也可以在基因组浏览器中呈现为图形。用户可以从查询结果中找到有用的注释，包括SNP类型，如同义或非同义SNP、剪接变体的起始和终止、染色体位置以及与植物基因组数据库（www.phytozome.net）高粱基因组数据库注释的链接。此外，网站上还可以找到与高粱研究相关的一般信息，如在线高粱资源和文献参考。所有SNP数据和注释均可从网站免费下载。
SorGSD是一个综合网站门户，提供了涵盖所有栽培高粱种族类型和野生近缘种的大规模基因组变异数据库。它可以作为高粱和其他C4禾本科植物一系列基因组学和分子育种活动的生物信息学平台。
