SorGSD: a sorghum genome SNP database

doi:10.1186/s13068-015-0415-8

CORC > 北京大学 > 生命科学学院

	SorGSD: a sorghum genome SNP database
	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
刊名	BIOTECHNOLOGY FOR BIOFUELS
	2016
关键词	Sorghum Bio-energy plant Genome variation SNPs Database curation DNA-SEQUENCING DATA WIDE ASSOCIATION BIOENERGY CROPS GRAIN-SORGHUM DISCOVERY BICOLOR MODEL FRAMEWORK GRASSES SYSTEM
DOI	10.1186/s13068-015-0415-8
英文摘要	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.; National Natural Science Foundation of China [31461143023, 31271797]; National Science and Technology Support Program [2015BAD15B03, 2013BAD22B01]; Sino-Africa Centre of CAS International Outreach Initiatives; SCI(E); EI; PubMed; ARTICLE; hcjing@ibcas.ac.cn; luojc@pku.edu.cn; 1; 6; 9
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/435457]
专题	生命科学学院
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.
APA	Luo, Hong.,Zhao, Wenming.,Wang, Yanqing.,Xia, Yan.,Wu, Xiaoyuan.,...&Luo, Jingchu.(2016).SorGSD: a sorghum genome SNP database.BIOTECHNOLOGY FOR BIOFUELS.
MLA	Luo, Hong,et al."SorGSD: a sorghum genome SNP database".BIOTECHNOLOGY FOR BIOFUELS (2016).