Genome-wide association study in historical and contemporary U.S. winter wheats identifies height-reducing loci

Plant height has been a major target for selection of high-yielding varieties in wheat. Two height-reducing loci (Rht-B1 and Rht-D1) have been widely used since the Green Revolution. However, these genes also negatively affect other agronomic traits such as kernel weight. Identifying alternative height-reducing loci could benefit wheat improvement. This study focused on the genetics of plant height in 260 historical and contemporary winter wheat accessions via genome-wide association studies using 38,693 single nucleotide polymorphism (SNP) markers generated through genotyping by sequencing, two Kompetitive Allele Specific Polymorphism markers, and phenotypic data recorded in two seasons (2016 and 2018). The 260 accessions showed wide variation in plant height. Most accessions developed after 1960 were shorter than earlier accessions. The broad-sense heritability for plant height was high (H² = 0.82), which was also supported by a high correlation (r = 0.82, P < 0.0001) between heights from the two years. We detected a total of 16 marker–trait associations (MTAs) for plant height at –lg (P) ≥ 4.0 on chromosomes 1A, 2B, 2D, 3B, 4D, 5A, 5D, 6A, 6B, 7A, and 7D. We detected three of the MTAs (QPLH-2D, QPLH-4B.2, and QPLH-4D) consistently in individual-year and combined-year analyses. These MTAs individually explained 10%–16% of phenotypic variation. The height-reducing alleles at these three MTAs appeared after 1960 and increased in frequency thereafter. Among the genes near these loci were gibberellic acid insensitive (GAI) and GRAS transcription factor (GIBBERELLIC-ACID INSENSITIVE (GAI), REPRESSOR of GAI (RGA), and SCARECROW (SCR)). The evidence from this study and previous reports suggests that QPLH-2D is Rht8. A gene encoding a GRAS transcription factor is located near QPLH-2D. Validation of the QPLH-2D locus and associated candidate genes awaits further study.