Using the mapping resource along with the phenotypic data we identified important QTLs for yield-related trait. A major stable QTL for kernel number per spike (KNPS; qKnps-4A) was verified in 10 environments by using MapQTL 6.0, IciMapping 4.1, and QTLNetwork 2.0 (Table 1; Fig. 4; Figures S5, S6). qKnps-4A contributed to 8.0–21.2% of the KNPS phenotypic variation in the 188 KJ-RILs, with alleles from J411 increasing kernels per spike by 1.2–2.4. The QTL peaks of qKnps-4A were in 149.8–155.0 cM, 149.7–154.5 cM, and 149.8 cM, as detected by MapQTL 6.0, IciMapping 4.1, and QTLNetwork 2.0, respectively, with Ax-109844107–Ax-110540586 in 149.6–150.3 cM in the overlapping confidence intervals. Thus, we predicted that the candidate genes for qKnps-4A might be within the overlapping confidence intervals of 0.7 cM. Based on the genome assembly of T. aestivum cv. CS (https://urgi.versailles.inra.fr/download/iwgsc/IWGSC-WGA_Sequences/), the overlapping confidence intervals of Ax-109844107–Ax-110540586 spanned 3.23 Mb (4 A:680398739–4 A:683638403) in physical position (Figure S7). This region harbours 65 predicted genes in wheat (Figure S8), which might include the candidate gene for qKnps-4A.Table 1 qKnps-4A as detected by MapQTL 6.0, IciMapping 4.1, and QTLNetwork 2.0.SoftwareLOD valuePosition (cM)Additive effectPVE %MapQTL 6.03.4 to 9.7149.8 to 155.0−1.5 to −2.48.0 to 21.2IciMapping 4.12.8 to 16.8149.7 to 154.5−1.2 to −2.49.5 to 20.3QTLNetwork 2.0 P value: 0.000000149.8−1.910.9 Figure 4Overlapping confidence intervals of QTLs for kernel number per spike (KNPS) based on MapQTL 6.0, IciMapping 4.1 and QTLNetwork 2.0. The segments in red are the overlapping confidence intervals of qKnps-4A, and the overlapping flanking markers of qKnps-4A are indicated by triangles in red, which were detected by QTLNetwork 2.0 based on the combined 10 environmental phenotypic values.