The First Phase of a Comprehensive Genetic Analyzing Platform for Rice: Establishment of an Integrated Genotype Database of Diverse Rice Genetic Resources

Rice is an important crop species of diverse and structured genetic characteristics. The rapid development of high throughput genotyping techniques allowed researchers to obtain exhaustive genetic information of the species. The global/local gerplasm collections and the development of multi-parent advanced generation inter-cross (MAGIC) populations have expedited the progress of genetic research and breeding in rice. However, limited by the diverse genotyping platforms applied in each panel, researchers were not able to bring out more comprehensive comparisons between each panel.

This study aims to undertake an aggressive approach to integrate the massive public and private genotype data of diverse populations and construct a comprehensive rice haplotype map (Hapmap) database. We include the genotyping by sequencing (GBS) data of ~350 reciprocal RILs of Nipponbare and IR64, a local collection of ~500 South East Asia accessions, MAGIC japonica population and the 60M array-based SNP data of ~400 global accessions. Reanalysis of GBS data generates a set of common SNP markers among diverse panels. This common SNP dataset is then merged with the 60M array-based marker set to form a high density genotype data. Two-step imputation is undertaken: 1) among natural accessions and the founder lines of intercross population; 2) within each intercross population. Similarly, independent haplotype reconstructions among natural germplasm and within each intercross population are conducted.

This high density SNP derived hapmap will be implemented in a web-based analyzing platform. This platform would potentially serve as a powerful tool for genetic researchers and breeders.