A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Secale cereale L.)

Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseqTM as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseqTM markers in the recently established ‘Lo7’ reference genome assembly. We identified cross-validated SNPs in ‘Lo7’ protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.