GWAS From Spoken Phenotypic Descriptions: A Proof of Concept From Maize Field Studies

Abstract

ABSTRACTSpeech-derived phenotypic descriptions analyzed using existing Genome-Wide Association Study (GWAS) methods recover genomic regions involved in the maize plant height trait, demonstrating that non-structured, spoken descriptions of phenotypes can be used for association genetics. We collected phenotypes ofZea maysby recording spoken descriptions of plant traits such as height, color, leaf width, and feel of the texture of the leaves. To examine the relevance of spoken phenotypic descriptions for association genetics, we phenotyped the Wisconsin Diversity panel and developed two methods to process these spoken descriptions, in this case, for plant height. To measure semantic similarity, we generated a score that indicates how alike each observation is in meaning to the query “tall”. For the second method, we binned manually scored phrases related to plant height, then assigned scores to each observation. These were compared to published genomic locations associated with plant height (and with data we manually collected). Both methods recover known plant height associations.