Abstract
Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice.
Highlights
Rice (Oryza sativa) was the first crop species selected for whole genome sequencing because of its relatively small genome size [1] and its global importance in food production [2, 3]
It is common for multiple amplicons to be observed for simple sequence repeat (SSR) markers and bands outside of expected size ranges are often ignored in allele calling
The development of a fully automated pipeline for determining pseudomolecule assembly positions of SSRs will be useful to overlay marker information on additional de novo assemblies of other rice accessions or other species as they become available. This will help maintain a connection between the latest genomic discoveries and the extensive body of rice genetics literature
Summary
Rice (Oryza sativa) was the first crop species selected for whole genome sequencing because of its relatively small genome size [1] and its global importance in food production [2, 3]. Draft genome sequences for rice were first produced in 2002 [4, 5], followed by a map-based, nearly complete genome sequence [6], and culminating in the release of a high-quality genome assembly with gene annotation [7]. The high-quality reference genome has enabled high-density genotyping [8, 9] and resequencing of over 3000 additional rice varieties [10, 11]. The availability of genomic and high-density genotyping data will be of tremendous value for rice genetics and breeding. Due to the size and structure of the datasets, working with these data is challenging for many field and bench scientists.
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