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2016;9 6.

SorGSD: a sorghum genome SNP database.

Hong Luo, Wenming Zhao, Yanqing Wang, Yan Xia, Xiaoyuan Wu, Limin Zhang, Bixia Tang, Junwei Zhu, Lu Fang, Zhenglin Du, Wubishet A Bekele, Shuaishuai Tai, David R Jordan, Ian D Godwin, Rod J Snowdon, Emma S Mace, Hai-Chun Jing, Jingchu Luo
Author Information
  1. Hong Luo: Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
  2. Wenming Zhao: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  3. Yanqing Wang: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  4. Yan Xia: Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
  5. Xiaoyuan Wu: Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
  6. Limin Zhang: Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
  7. Bixia Tang: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  8. Junwei Zhu: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  9. Lu Fang: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  10. Zhenglin Du: Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
  11. Wubishet A Bekele: Department of Plant Breeding, Justus Liebig University, Giessen, Germany.
  12. Shuaishuai Tai: BGI-Shenzhen, 518083 Shenzhen, China.
  13. David R Jordan: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD 4370 Australia.
  14. Ian D Godwin: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia.
  15. Rod J Snowdon: Department of Plant Breeding, Justus Liebig University, Giessen, Germany.
  16. Emma S Mace: Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD 4370 Australia.
  17. Hai-Chun Jing: Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
  18. Jingchu Luo: College of Life Sciences and State Key Laboratory of Protein and Plant Gene Research, Peking University, 100871 Beijing, China.
PMID: 26744602 DOI: 10.1186/s13068-015-0415-8

Abstract

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, ~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 C4 grasses.

Keywords

Bio-energy plant Database curation Genome variation SNPs Sorghum

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Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC001792 (SorGSD)

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