Abstract
Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range from large generic databases which hold specific data types for a broad range of species, to carefully integrated and curated databases which act as a resource for the improvement of specific crops. In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome databases.
Highlights
The majority of DNA sequence and expressed gene sequence data generated today comes from the next- or second-generation sequencing (NGS/2GS) technologies
Molecular genetic markers technologies such as restriction fragment length polymorphisms have been replaced by more high throughput methods, including amplified fragment length polymorphisms (AFLPs), diversity array technologies (DArT) and simple sequence repeats (SSRs) known as microsatellites
single-nucleotide polymorphisms (SNPs) at any particular site could in principle involve four different nucleotide variants, but in practice they are generally biallelic
Summary
The majority of DNA sequence and expressed gene sequence data generated today comes from the next- or second-generation sequencing (NGS/2GS) technologies. Genomics is undergoing a revolution, driven by advances in DNA sequencing technology, and this data flood is having a major impact on approaches and strategies for crop improvement. Agronomy 2012, 2 been applied for sequenced genomes of a number of cereal crop species including rice, Sorghum and maize. Numerous databases have been developed for genomic data, on a range of platforms and to suite a variety of different purposes (see Table 1 for examples). These range from generic DNA sequence or molecular marker databases, to those hosting a variety of data for specific species
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