SorGSD: a sorghum genome SNP database.
SorGSD: a sorghum genome SNP database.
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SorGSD：高粱基因组SNP数据库
DOI：
10.1186/s13068-015-0415-8
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发表时间：
2016
影响因子：
6.3
通讯作者：
Luo J
中科院分区：
文献类型：
--
作者：
Luo H;Zhao W;Wang Y;Xia Y;Wu X;Zhang L;Tang B;Zhu J;Fang L;Du Z;Bekele WA;Tai S;Jordan DR;Godwin ID;Snowdon RJ;Mace ES;Jing HC;Luo J
高粱是世界上最重要的粮食作物之一，也是一种潜在的生产生物燃料的能源植物。为了探索一系列重要数量性状的遗传增益，如耐旱性和耐热性，谷物产量，茎糖积累和生物量生产，通过使用分子育种和基因组选择策略，可用的遗传变异和潜在的序列多态性的知识，是必需的。基于组装和注释的两色高粱基因组序列（v2.1）和最近发表的高粱重测序数据，在48份高粱种质中鉴定出约62.9M SNP，并将其纳入新开发的高粱基因组SNP数据库SorGSD（sorgsd.big.ac.cn）。48个高粱品系的多样性面板可以分为四个组，改良品种，地方品种，野生和杂草高粱，和野生近缘高粱。SorGSD有一个基于网络的查询界面，可以搜索或浏览来自单个登录的SNP，或者比较几个品系之间的SNP。查询结果可以可视化为表格中的文本格式，或者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的类型，例如同义或非同义SNP，剪接变体的开始和停止，染色体位置，以及到Phytozome（www.phytozome.net）高粱基因组数据库注释的链接。此外，与高粱研究相关的一般信息，如在线高粱资源和参考文献也可以在网站上找到。所有的SNP数据和注释都可以从网站上免费下载。SorGSD是一个综合性的门户网站，提供了一个大规模的基因组变异数据库，涵盖了所有栽培高粱和野生高粱的种族类型。它可以作为高粱和其他C4禾本科植物的一系列基因组学和分子育种活动的生物信息学平台。
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.