CerealsDB 3.0: Expansion of Resources and Data Integration

BMC Bioinformatics. 2016 Jun 24;17:256. doi: 10.1186/s12859-016-1139-x.

Abstract

Background: The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the most important crops in human and livestock diets, and the development of wheat varieties that produce higher yields, combined with increased resistance to pests and resilience to changes in climate, has meant that wheat breeding has become an important focus of scientific research. In an attempt to facilitate these improvements in wheat, plant breeders have employed molecular tools to help them identify genes for important agronomic traits that can be bred into new varieties. Modern molecular techniques have ensured that the rapid and inexpensive characterisation of SNP markers and their validation with modern genotyping methods has produced a valuable resource that can be used in marker assisted selection. CerealsDB was created as a means of quickly disseminating this information to breeders and researchers around the globe.

Description: CerealsDB version 3.0 is an online resource that contains a wide range of genomic datasets for wheat that will assist plant breeders and scientists to select the most appropriate markers for use in marker assisted selection. CerealsDB includes a database which currently contains in excess of a million putative varietal SNPs, of which several hundreds of thousands have been experimentally validated. In addition, CerealsDB also contains new data on functional SNPs predicted to have a major effect on protein function and we have constructed a web service to encourage data integration and high-throughput programmatic access.

Conclusion: CerealsDB is an open access website that hosts information on SNPs that are considered useful for both plant breeders and research scientists. The recent inclusion of web services designed to federate genomic data resources allows the information on CerealsDB to be more fully integrated with the WheatIS network and other biological databases.

Keywords: CerealsDB; Database; Genomic selection; SNPs; Single nucleotide polymorphisms; Wheat.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breeding
  • Crops, Agricultural / genetics
  • Database Management Systems
  • Genomics
  • Genotyping Techniques
  • Humans
  • Internet
  • Polymorphism, Single Nucleotide*
  • Triticum / genetics*
  • User-Computer Interface