In JMP Genomics, the Relationship Matrix analysis is used for computing and displaying relatedness among lines. The Relationship Matrix tool estimates the relationships among the lines using marker data, rather than pedigree information (Kinship Matrix tool), and computes the relationship measures directly while also accounting for selection and genetic drift. The Relationship Matrix computes one of three options: Identity-by-Descent, Identity-by-State, or Allele-Sharing-Similarity. Output from this procedure can serve as the K matrix, representing familial relatedness, in a Q-K mixed model. This post will focus on the Relationship Matrix using a data set containing 343 rice lines with 8,336 markers.
K-Matrix Compression (optional)
Q-K association analysis is computationally intensive and the part incorporating the K matrix is especially time-consuming. There is a technique for reducing the number of variables required to represent the familial relatedness between lines. With fewer variables each model, run time is significantly reduced. The technique is called K Matrix Compression. It can be performed in JMP Genomics as part of the Genetics Q-K Analysis Workflow (which you can learn about in a later blog post), or as a free-standing process. The algorithm optimizes the compression for one trait variable at a time, so it needs to be repeated for each trait to be analyzed.
*The interactive results from this analysis are available on JMP Public.
This document served as a walkthrough for creating a Relationship Matrix from a data set containing 343 rice lines with 8,336 markers. This relationship matrix was composed of Identity By Descent values, but can be calculated for Identity By State and Allele Sharing Similarity as well. This process estimated the relationships among the lines using marker data since no pedigree information was available. Additionally, this post covered K-Matrix Compression, which can be used to reduce computing time in Q-K Association Analysis while still producing similar results to analysis with an uncompressed matrix.