A century of breeding has preserved genetic variation, accumulated favorable alleles, and shaped the Rht gene portfolio in North American spring wheat

Abstract

Hard red spring wheat (HRSW) is an important market class of wheat in North America with a rich history of breeding. We genotyped 1,013 HRSW lines representing a century of breeding material using a SNP array and targeted KASP genotyping to assess the changes in genetic diversity and Rht genes in HRSW from North America. Results show that early breeding efforts broadened an initially narrow gene pool derived from a few founders and subsequently maintained the genetic diversity. Analysis of Rht genes revealed that Rht-D1b was the predominant semi-dwarf allele from introduction of the Green Revolution genes (Rht-B1 and Rht-D1) in 1960s until the FHB epidemics of 1990s, when most breeding programs shifted to Rht-B1b. However, adoption of Rht-B1b and Rht-D1b remains low in some regions of the Great Plains. The dwarf alleles at GA-sensitive Rht24 and Rht25 have persisted in the region at low frequencies before the introduction of Green Revolution genes and have increased in frequency in recent decades. We also analyzed the effect of Rht genes on plant height (PH) in the HRSW growing region and found that Rht-B1b or Rht-D1b results in [~]12% reduction in PH, which decreases to [~]9% in dry environments. Notably, combining dwarfing alleles at Rht24 and Rht25 reduced height by [~]6% in dry environments, suggesting an alternative approach for reducing PH. Our analysis also revealed significant genetic interactions between Rht-B1 and Rht25, as well as between Rht-D1 and Rht24, which could help fine-tune PH for different environments by employing appropriate Rht combinations. Furthermore, our results demonstrate positive selection for photoperiod sensitivity in recent decades, particularly in high-latitude regions. This study provides a valuable genomic resource, and the findings enhance our understanding of past breeding efforts while offering insights to guide future plant breeding strategies.