Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass

• Main Authors: Stephen L. Byrne, Patrick Conaghan, Susanne Barth, Sai Krishna Arojju, Michael Casler, Thibauld Michel, Janaki Velmurugan, Dan Milbourne
• Format: Article
• Language: English
• Published: Nature Publishing Group 2017-06-01
• Series: Scientific Reports
• Online Access: https://doi.org/10.1038/s41598-017-03232-8

Abstract Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.