Rice Haplotype Map Project Database
(Second Generation)
Home | Genotype Dataset | SNP Information | Assembly and Variants | GBrowse | Blast | Software

National Center for Gene Research, CAS

Now the second generation rice haplotype map is available, with world-wide rice cultivars added and assembly sequences released. The sample here includes 620 Chinese landraces and 330 diverse global cultivars from 33 countries. The germplasm collection was sequenced on the Illumina Genome Analyzer IIx, with approximate one-fold coverage for each. The resulting sequence dataset of 950 rice varieties consisted of 4.6 billion of 73-bp paired-end reads. The long term goal of this project is to develop a comprehensive platform to unravel the genetic diversity of cultivated rice and facilitate the genetic mapping of complex traits, to assist genetic study and improvement of the dramatically important crop.

The data of low-coverage sequencing of rice diverse varieties can be cited:

  • Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B. Genome-wide association study of flowering time and grain yield traits in a world-wide collection of rice germplasm. Nat. Genet. 44: 32–39 (2012).
  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, Han B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42: 961-967 (2010).

Genotype Dataset
The genotype dataset includes the set of 950 varieties, the subset of 508 indica accessions and the subset of 383 japonica accessions. The genotype dataset can be found at the Genotype Section (http://www.ncgr.ac.cn/RiceHap2/Geno.php).

SNP Information
The collection has five divergent groups – indica, aus, temperate japonica, tropical japonica (also named javanica) and intermediate, from which a total of 4,109,366 non-singleton SNPs were identified. The details of the 4.1 million SNPs, including their position and allele frequencies in each population, are available at http://www.ncgr.ac.cn/RiceHap2/SNPs.php.

Assembly and Variants
Here we provide local assembly sequences for Chinese landraces. A haplotype-based local sequence assembly method was used in the assembly process, which combines sequencing reads of a common haplotype in a local region to perform de novo assembly. The local assembly sequences, complex variant dataset (including detailed annotations) and BLAST searching are available at http://www.ncgr.ac.cn/RiceHap2/Assembly.php.

GBrowse
The second generation rice haplotype map can be also visited through Genome Browse searching (http://www.ncgr.ac.cn/RiceHap2/GBrowse.php). The reference sequence in the Browse is IRGSP Build 4.0. The set of 950 varieties, the subset of 508 indica accessions and the subset of 383 japonica accessions are all available in Genome Browse.

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