Data Management and Analysis System for Genetic Association Studies of Rice

Bioinformatics RIG and Indonesian Center for Agricultural Biotechnology & Genetic Resources has been collaborate in developing “Data Management and Analysis System for Genetic Association Studies of Rice“. The system has brought as much as 1536 – associated SNP genotyping with phenotyping associations related to the character of the age and yield components. It also includes 384-related SNPs identification and development of identity-based selection system varieties or germplasm. Associated with the 384 – SNP, at IRRI was utilized for the identification and tracing of rice crosses of Indica-Indica , Japonica-Japonica and Indica-Japonica . Meanwhile in BB Biogen , the selection / filtering 1536-SNP scattered in 12 chromosome.

This web-based system is also equipped with a data dictionary , which includes : SNP map , sample map, the final report and phenotype. SNP map contains the genetic information of the markers that have been used, namely 1536-SNP and 384-SNP. Some information related SNP map is : SNP ID, chromosome, genetic position in the rice genome and gene train . Sample map contains information about the total germplasm accessions were used , namely 467 and 288 accessions. Some information related to the sample folder is : no.index , ID germplasm , genetic background and sentrix position . Final report contains profile information genotype / DNA fingerprinting 467 and 288 germplasm accessions of rice by 1536- SNP and 384- SNP. Phenotype contains phenotypes information profile of 467 and 288 accessions of rice germplasm for morphological characters and yield components.

This research is funded by the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Indonesia (2012-2014).