Genetic dissection for seedling root-related traits using multiple-methods in bread wheat (Triticum aestivum L.)

Several quantitative trait loci (QTL) and structural chromosome variations (SCVs) related to seedling root traits were identified using multiple methods, which provided valuable insights to assist breeding efforts in wheat. The root system of wheat affects water and fertilizer use efficiency, stress tolerance, and agronomic traits. Using association analysis and linkage mapping, QTL associated with 11 seedling-stage root traits were identified with single nucleotide polymorphisms (SNPs) and SCVs under both hydroponic nutrient solution culture experiment (NCE) and vermiculite culture experiment (VCE). Except for maximum root length (MRL), the root traits of seedlings under NCE and VCE differed significantly. Root fresh weight (RFW) and root dry weight (RDW) were significantly correlated with most agronomic traits and grain yield. Identification of RFW and RDW by NCE might provide a reference basis for VCE. Co-localization analysis revealed that NCE and VCE simultaneously detected SNP-loci viz. QRdw.sxau-6A, QRd.sxau-1B.2, and QDw.sxau-6A (5.56-8.76% of R²). The SCV-loci Mr1B-3, Mr3A-3 and Mr3A-4 were detected in both NCE and VCE (4.74-9.07% of R²). Furthermore, QRdw.sxau-6A, QSfw.sxau-6A and QRd.sxau-4A were detected using the mixed linear model (MLM), 3 Variance-component multi-locus random-SNP-effect Mixed Linear Mode (3VmrMLM) and rrBLUP. In the association panel, SNPs and SCVs co-localized to 14 MTAs, of which Mr5A-6 and QRd.sxau-5A were significantly associated with root diameter (RD). The association panel and doubled haploid (DH) population co-located 10 QTL, of which QDw.sxau-1D was stably detected. Finally, QDw.sxau-6A and Mg6A-9 overlapped in same genomic location containing candidate genes TraesCS6A02G372300, TraesCS6A02G382900 and TraesCS6A02G365100. The present study contributes novel insights into the genetics of root architecture in wheat.