AlleleDB

AlleleDB provides tools and datasets for exploring allelic variation and combination at agriculturally important loci. The database supports visualization of multi-locus allele combinations through AlleleGraph and allele classification using genome-wide polymorphism data.

The current release focuses on rice and provides demo datasets for AlleleGraph as well as the Rice Allele Collection, a reference population for allele classification.

AlleleGraph

AlleleGraph is a versatile visualization tool applicable to a wide range of agricultural species, including cereals, fruit trees, and vegetables, enabling users to examine allele combinations at multiple loci together with phenotypic data.

Open the latest AlleleGraph

Input data for AlleleGraph

AlleleGraph accepts three types of input data:

Graph data (required)
Phenotype data (optional)
Allele effect data (optional)

1. Graph data (required)

The first row is a header row, the first column is ID, the second column is Name, and the third and subsequent rows are loci information. In addition to Locus ID and Name, locus information can include location information, each of which is separated by a vertical bar. Positional information is indicated as “Chromosome Name:Position. The second and subsequent lines contain the ID or Name of each variety or strain and the allele type of each locus.

ID	NAME	Os06t0275000-01\|Hd1\|chr06:9336376	Locus name B	Locus name C	...
RAC-001	Koshihikari	allele1	allele1	allele1	...
RAC-002	Hinohikari	allele1	allele1	allele1	...
...	...	...	...	...	...
RAC-025	Nipponbare	allele2	allele2	allele2	...
RAC-026	Sasanishiki	allele2	allele2	allele2	...
...	...	...	...	...	...

2. Phenotype data (optional)

The first line is a header line, the ID column is required, and the second and subsequent columns are phenotype names. If the phenotype is categorical data, add “|c” after the phenotype name. After the second line, the first column is the ID of the variety or strain, and the second and subsequent columns are the phenotype data (numeric or categorical data).

ID	VARIETY\|c	FloweringTime	...
RAC-001	TEJ	87	...
RAC-002	TEJ	112	...
...	...	...	...
RAC-025	TEJ	102	...
RAC-026	TEJ	84	...
...	...	...	...

3. Allele effect data (optional)

Locus ID	Allele	Phenotype	Effect,SE
Os06t0275000-01	allele1	FloweringTime	4.12,12.61
Os06t0275000-01	allele2	FloweringTime	-10.85,12.79
...	...	...	...
Locus name B	allele1	FloweringTime	-6.61,15.25
Locus name B	allele2	FloweringTime	2.01,14.84
...	...	...	...

Demo data for AlleleGraph

Rice Allele Data provides sample datasets for AlleleGraph. It includes allele information from the Rice Allele Collection for 10 heading date-related genes and 10 genes associated with diverse agronomic traits such as heading date, eating quality, and grain shape.

Graph data for 10 flowering-related rice genes

Graph data for 10 agronomic trait-related rice genes

Phenotypic data for RAC

Rice allele collection

Rice Allele Collection (RAC) is a set of 230 rice cultivars and breeding materials designed to support allele classification and to organize allelic variation found in useful domestic cultivars and breeding materials.

Allele classification tool

Allele Classification Tool enables to classify alleles at target loci from genome-wide variant data in multi-sample VCF format across multiple varieties and lines. This tool is currently under development.