IC4R006-GWAS-2015-25689273

Project Title

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

The Background of This Project

figure 1 Population structure of current association panel which consisted mostly of the indica accessions. (A) Scree plot from GAPIT showing the selection of PCs for association study. (B) PCA plot of first two components. (C) Bayesian clustering of 220 rice accessions using STRUCTURE program.

Research Findings

Figure 2 Comparison of LD patterns and LD decay in the whole panel and subgroups. The whole genome r 2 values from PLINK are first sorted considering distance, and then divided into 100 blocks of 20 kb. The r 2 values in each block are averaged and plotted against the genetic distance for different subgroups.

Labs working on this Project

• Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
• International Rice Research Institute, Los Baños, Philippines
• International Center for Tropical Agriculture, Cali, Colombia
• Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
• US Department of Agriculture—Agricultural Research Service (USDA-ARS), Ithaca, New York, United States of America

Corresponding Author

• Jean-Luc Jannink(jj332@cornell.edu)
• Susan R. McCouch(srm4@cornell.edu)