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

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 12 seedling-stage root traits were identified with SNPs and SCVs under both hydroponic nutrient solution culture experiment (NCE) and soil culture experiment (SCE). Except for MRL, the root traits of seedlings under NCE and SCE differed significantly. Several seedling indicators, including RFW, RDW and RS, were significantly correlated with adult plant agronomic traits. Identification of RFW, RDW, RS, and RV by NCE is equivalent to SCE for subsequent research. Under NCE, 29 stable loci and 9 SCVs of 12 root traits were detected respectively by SNPs and SCVs association analysis. Under SCE, association analysis detected 23 stable loci with SNPs and 26 loci with SCVs. In the DH population, 21 stable QTL were detected by SNPs linkage analysis, and 6 SCVs were found by SCVs analysis. Co-localization analysis revealed that NCE and SCE simultaneously detected QRdw.sxau-6A, QRd.sxau-1B.2, and QDw.sxau-6A (5.56%-8.76% of R2). Mr1B-3, Mr3A-3 and Mr3A-4 were detected in both NCE and SCE (4.74%-9.07% of R2). In the association panel, SNPs and SCVs co-localized to 14 MTAs, of which Mr5A-6 and QRd.sxau-5A were significantly associated with RD. The association panel and DH population co-located 10 QTL, of which QDw.sxau-1D was stably detected. 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.