Genome-wide association study on ten traits of economic importance in hop (Humulus lupulus L.)

Abstract

Hop is used primarily for bittering and flavoring of beer although new uses of hop have been implemented in poultry production, sugar processing and pharmaceuticals. Traditional hop breeding is a lengthy, expensive process. Modern selection methods such as marker-assisted selection are needed to greatly improve genetic gains per selection cycle as well as reduce the number of experimental lines evaluated in the field. Recent implementation of next generation sequencing enables the scanning of whole genomes for markers linked to traits of interest using an analysis called genome-wide association studies (GWAS). This study was initiated to identify markers associated with expression of 10 different traits in hop. Illumina Inc. technology sequencing of 116 genetically distinct hop cultivars from multiple regions of the world was performed. SNP marker identification was achieved using the TASSEL v3.0 UNEAK pipeline. Filtering of SNP markers resulted in a working group of 32,206 SNP markers screened across all 116 cultivars. Phenotypic data for all cultivars were collected over a 35-year period and data from four years were used. Mixed linear models analyses in TASSEL v5.0.0 were used for five of the traits while the remaining five traits were evaluated using general linear models. A total of 86 SNP markers were identified and reported as significantly associated with one of the 10 traits. Heritability for traits matched with those previously published. This is the first reported genome wide association study in hop and as such represents an important step forward in aiding marker assisted selection. Nevertheless, it remains that further validation of these SNP markers is needed prior to implementation in a breeding program.