Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: https://ngdc.cncb.ac.cn/sorgsd
Full name: a sorghum genome SNP database
Description: SorGSD is a comprehensive database of sorghum genomic variations (SNPs and INDELs) of 289 accessions, phenotypes, practical tools, resources and critical references
Year founded: 2015
Last update: 2021
Version: 2.0
Accessibility:
Manual:
Accessible
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Country/Region: China

Classification and Labelling

Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: No.1 Beichen West Road, Chaoyang District
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Wenming Zhao/Huaiqing Hao
Contact email (PI/Helpdesk): zhaowm@big.ac.cn

Publications

34344425
SorGSD: updating and expanding the sorghum genome science database with new contents and tools. [PMID: 34344425]
Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W, Hao H, Jing HC.

Background

As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits.

Results

We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/ .

Conclusions

SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.

Biotechnol Biofuels. 2021:14(1) | 1 Citations (from Europe PMC, 2022-05-14)
26744602
SorGSD: a sorghum genome SNP database. [PMID: 26744602]
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.

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.

Biotechnol Biofuels. 2016:9() | 17 Citations (from Europe PMC, 2022-05-14)

Ranking

All databases:
2196/5177 (57.601%)
Raw bio-data:
177/510 (65.49%)
Gene genome and annotation:
645/1407 (54.229%)
Genotype phenotype and variation:
315/752 (58.245%)
Literature:
185/435 (57.701%)
2196
Total Rank
18
Citations
3
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Record metadata

Created on: 2016-05-06
Curated by:
Dong Zou [2021-09-16]