3.4.2. Plant Height (PH)

We found three QTLs (*qPH1.1, qPH6.1* and *qPH7.1*) related to PH in the CSSLs, which were distributed on chromosome 1, 6 and 7, respectively. Five CSSLs (RZ14, RZ16, RZ17, RZ92, RZ105, RZ107 and RZ164) had PH values of 170 ± 9 cm, while 93-11 plants were about 110 ± 5 cm (Figure S2D). *qPH1.1* was identified in the overlapping segmen<sup>t</sup> of RZ14, RZ16, RZ17 and the *Sd1* was in the same position [37]. The RZ92 and RZ164 segments overlapped near the molecular marker C6-8 on chromosome 6 and the *qPH6.1* was identified in this region. The *qPH7.1* was identified in the overlapping segments of RZ105 and RZ107 near the molecular marker C7-5 on chromosome 7 (Table 3; Figure S6).

### 3.4.3. Number of Grains per Panicle (NGPP) and 100 Grain Weight (GWT)

We identified three QTLs (*qNGPP3.1, qNGPP4.1* and *qNGPP12.1*) related to NGPP that were distributed on chromosome 3, 4 and 12. Seven CSSLs (RZ51, RZ50, RZ52, RZ64, RZ20, RZ144 and RZ145) had more than 210 NGPP while 93-11 had less than 180 NGPP in both seasons (Figure 4A). We identified QTL *qNGPP3.1* in C3-19 and *qNGPP4.1* in C4-12. An overlapping segmen<sup>t</sup> in C12-2 contained a QTL named *qNGPP12.1* (Table 3; Figure S6).

### 3.4.4. Grain Length (GL), Grain Width (GW) and Grain Length to Width Ratio (GLWR)

Two QTLs (*qGL3.1* and *qGL9.1*) related to GL were detected in the CSSLs on chromosome 3 and 9. Three CSSLs (RZ3, RZ49 and RZ50) had GLs of 8.40 ± 0.06 mm, while 93-11 had a GL of 10.03 ± 0.13 mm (Figure 4B). The RZ49 and RZ50 segments overlapped near the molecular marker C3-19 on chromosome 3 and this new QTL was named *qGL3.1*. The QTLs *qGL9.1* and *SG1* were detected in the segmen<sup>t</sup> of RZ3 near the molecular marker C9-12 on chromosome 9 [39] (Table 3; Figure S6).

Two QTLs (*qGW9.1* and *qGW10.1*) related to GW were detected on chromosome 9 and 10. Three CSSLs, (RZ133, RZ3 and RZ134) had GWs of less than 2.85 mm, while 93-11 had a GW of more than 2.98 mm (Figure 4B). The RZ3 segmen<sup>t</sup> was located near the molecular marker C9-8 on chromosome 9 and named *qGW9.1*. We identified *qGW10.1* in the overlapping segmen<sup>t</sup> of RZ133 and RZ134, near the molecular marker C10-3 on chromosome 10 (Table 3; Figure S6).

**Figure 4.** Phenotypic variation in the appearance of grains and awns in CSSLs and 93-11. (**A**) Grain number per ear for RZ50 and 93-11 (bar = 10 cm); (**B**) length of grains of RZ3 and 93-11 (bar = 1 cm); (**C**) Phenotypes of the awns of RZ21, RZ68 and 93-11: (**A**) awn length (bar = 1 cm) and (**C**) awn tip surfaces of RZ68 and 93-11 (bar = 1 mm).

Two QTLs (*qGLWR3.1* and *qGLWR8.1*) related to GLWR were detected on chromosome 3 and 8, respectively. Three CSSLs, (RZ56, RZ111 and RZ167) had GLWRs of 3.5 while 93-11 had a GLWR of 3.3. The overlapping segments of RZ56 and RZ167 were found near the molecular marker C3-26 on chromosome 3 and named *qGLWR3.1*. We detected *qGLWR8.1* in the segments of RZ112, near the molecular marker C8-2 on chromosome 8 (Table 3; Figure S6).
