Combined Genome-Wide Association Studies (GWAS) and Linkage Mapping Identifies Genomic Regions Associated with Seedling Root System Architecture (RSA) under Different Nitrogen Conditions in Wheat (<i>Triticum aestivum</i> L.)

The nitrogen (N) use efficiency (NUE) in the roots of seedlings is beneficial for increasing crop yield. Creating marker-assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Exploring and identifying the effect of different N supply conditions on root system architecture (RSA) is of great significance for breeding N efficient wheat varieties. In this study, a total of 243 wheat varieties native to the Yellow and Huai Valley regions of China were utilized for genome-wide association studies (GWAS). Furthermore, a recombinant inbred line (RIL) population of 123 lines derived from the cross between Avocet and Chilero was utilized for linkage examination. A hydroponic seedling experiment using a 96-well tray was conducted in the lab with two treatments: normal N (NN) and low N (LN). Five RSA traits, including the relative number of root tips (RNRT), relative total root length (RTRL), relative total root surface area (RTRS), relative total root volume (RTRV), and relative average root diameter (RARD), were investigated. GWAS and linkage analysis were performed by integrating data from the wheat 660 k single nucleotide polymorphism (SNP) chip and diversity arrays technology (DArT) to identify genetic loci associated with RSA. The results showed that, based on the ratio of RSA-related traits under two N supply conditions, a total of 497 SNP markers, which are significantly associated with RSA-related traits, were detected at 148 genetic loci by GWAS. A total of 10 QTL loci related to RSA were discovered and identified by linkage mapping. Combining two gene localization methods, three colocalized intervals were found: <i>AX-95160997/QRtrl.haust-3D</i>, <i>AX-109592379/QRnrt.haust-5A</i>, and <i>AX-110924288/QRtrl.haust-7D/QRtrs.haust-7D</i>. According to the physical location of the colocalization of these two sites, between 39.61 and 43.74 Mb, 649.97 and 661.55 Mb, and 592.44 and 605.36 Mb are called <i>qRtrl-3D</i>, <i>qRnrt-5A,</i> and <i>qRtrl-7D</i>. This study has the potential to enhance the effectiveness of selecting root traits in wheat breeding programs, offering valuable insights into the genetic underpinnings of NUE in wheat. These results could help in breeding wheat varieties with higher NUE by implementing focused breeding strategies.