1. Overview

2. Data Description

3. Individual Source

  • Overview

    Sorghum is one of the most important global crops, which is produced as a source of food, feed, fiber and fuel. Its comparatively compact genome among C4 plants also makes it as an ideal model organism for comparative genomics studies. Recently, the genetic basis of some particular capacities of sorghum, such as high photosynthetic efficiency, drought resistance, and heat tolerance, have been elucidated by decoding its genome. Nevertheless, many agronomic traits of different sorghum lines vary greatly, in terms of plant height, stem sugar, juice accumulation, biomass production, and so on. For tailor-designed breeding and high efficiency genomic selection, genome-wide spectrum of the variations between sorghum lines is required. Recently, increasing number of sorghum accessions has been re-sequenced and large amount of SNP data were generated, which provides a good opportunity for researchers to compare genome variation between sorghum accessions, to explore the evolutionary relationship of cultivated and wild sorghum species and subspecies, to develop biomarkers for genetic studies, and to perform genome wide association studies (GWAS).

    To make a better use of these sorghum SNP data, we developed SorGSD, a web-based large scale genome variation database. SorGSD contains 62 million SNPs from a diverse panel of 48 sorghum accessions which were divided into four groups, including improved inbreds, landraces, wild/weedy sorghums, and a wild relative Sorghum propinquums. We made annotations for these data and designed an easy-to-use web interface for users to browse, search and analyze the SNPs efficiently. SorGSD allows users to query the SNPs information and their relevant annotations for each sorghum line. The search results can be either visualized graphically in a genome browser or displayed in formatted tables. Users can also perform comparison of these data between two or among several sorghum accessions. The output of query results of specific sets, or the whole SNP dataset of 48 accessions can be downloaded for further investigation. The high density of these SNP data at genomic level collected from the major races of cultivated sorghum as well as other subspecies is a rich repository a broader research community working in biomarker identification, genetic analysis and molecular breeding of sorghum and other crops.