Novel QTL Hotspots for Barley Flowering Time, Plant Architecture, and Grain Yield

Abstract

Barley (Hordeum vulgare L.) is one of the oldest cultivated grains and remains a significant crop globally. Barley breeders focus on developing high-yield cultivars resistant to biotic and abiotic stresses. Barley’s flowering time, regulated genetically and by environmental stimuli, significantly impacts all of its agronomic traits, including the grain yield and plant architecture. This study aimed to detect the quantitative trait loci (QTLs) affecting these traits in 273 two-row spring barley accessions from the USA, Kazakhstan, Europe, and the Middle East across two regions of Kazakhstan, evaluating their impact on grain yield. Genotypic data were obtained from 26,529 segregating single-nucleotide polymorphisms (SNPs), and field trial data for 273 accessions, which were obtained for six traits (heading time, maturity time, vegetation period, plant height, peduncle length, and grain yield) in two regions of Kazakhstan over three growth years. As a result of a genome-wide association study (GWAS), 95 QTLs were identified for 6 agronomic traits, including 58 QTLs linked with candidate genes and/or QTLs. The remaining 37 QTLs were putatively novel, with 13 of them forming 3 QTL hotspots on chromosomes 1H (5 QTLs in the interval of 13.4–41.4 Mbp), 3H (4 QTLs in 608.6–624.9 Mbp), and 6H (4 QTLs in 553.8–572.8 Mbp). These hotspots were pleiotropic, and targeting these regions would allow breeders to enhance multiple yield-associated traits.