Ricebase

Ricebase (https://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.
Resources in this dataset:Resource Title: Ricebase. File Name: Web Page, url: https://ricebase.org/ Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

Ricebase（https://ricebase.org）是一个专注于水稻（Oryza sativa）的整合基因组数据库，其核心在于以保持过去与当前遗传学研究之间关键联系的方式整合数据集。Ricebase涵盖了DNA序列数据、基因注释、核苷酸变异数据和分子标记片段大小数据。水稻研究得益于对简单序列重复（SSR）标记的早期采用和广泛使用；然而，大多数水稻SSR标记是在最新的水稻伪分子组装之前开发的。在引用SSR的文献背景下，对使用单核苷酸多态性（SNPs）的新研究进行解读时，需要有一个共同的坐标系。采用了一种新的管道，通过逐步放宽严格性，将SSR引物映射到最新的水稻伪分子组装上。SSR标记和实验测定的扩增子大小以关系数据库的形式呈现，并通过基于网络的界面提供，可作为基因组浏览器中的轨迹使用，浏览器与数据库之间通过链接相连。Ricebase的综合能力将遗传标记、基因组背景、水稻种质中的等位基因状态以及可能由用户编辑的表型解释相结合，作为一个社区资源，用于水稻的遗传发现和育种。